2024

Liao, J., Sergeeva, A.P., Harder, E.D., Wang, L., Sampson, J.M., Honig, B. and Friesner, R.A., (2024) A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding. J. Chem Theory and Comp.

20:8609-8623.Sampson, J.M., Cannon, D.A., Duan, J., Epstein, J.C.K., Sergeeva, A.P., Katsamba, P.S., Mannepalli, S.M., Bahna, F.A., Adihou, H., Guéret, S.M., Gopalakrishnan, R., Geschwinder, S., Rees, D.G., Siguradardottir, A., Wilkinson, T., Dodd, R.B., De Maria, L., Mobarec, J.C., Shapiro, L., Honig, B., Buchanan, A., Friesner, R.A. and Wang, L. (2024) Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations. JMB 436:168640.

Zhao, H., Murray, D., Petrey, D. and Honig, B. (2024) ZEPPI: Proteome-Scale Sequence-Based Evaluation of Protein-Protein Interaction Models.  Proc. Natl. Acad. of Sci. 21:e2400260121

Rosenberger, G., Li, W., Turunen, M., He, J., Subramaniam, P.S., Pampou, S., Griffin, A.T., Karan, C., Kerwin, P., Murray, D., Honig, B., Liu, Y. and Califano, A. (2024) Network-based Elucidation of Colon Cancer Drug Resistance Mechanisms By Phosphoproteomic Time-series Analysis. Nature Communciations. 15:3909.

2023

Nagendra, K., Izzet, A., Zakine, R., Friedman, L., Harrison, O.J., Pontani, L.-L., Shapiro, L., Honig, B. and Brujic, J. (2023) Push-pull Mechanics of E-cadherin Ectodomains in Biomimetic Adhesion. Biophysical J. 122:3506-3515.

Sergeeva, A.P., Katsamba, P.S., Liao, J., Sampson, J.M., Bahna, F., Mannepalli, S., Morano, N.C., Shapiro, L., Friesner, R.A. and Honig, B. (2023) Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J. Mol. Biol. 435:168187.

Trudeau, S.J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D. and Honig, B. (2023) PrePCI: A Structure- and Chemical Similarity-Informed Database of Predicted Protein Compound Interactions. Protein Science. e:4594.

Petrey, D., Zhao, H., Trudeau, S., Murray, D. and Honig, B. (2023) PrePPI: A Structure Informed Proteome-Wide Database of Protein-Protein Interactions. J. of Mol. Biol. 435:168052.

Su, Z., Kon, N., Yi, J., Zhao, H., Zhang, W., Tang, Q., Li, H., Kobayashi, H., Li, Z., Duan, S., Liu, Y., Olive, K.P., Zhang, Z., Honig, B., Manfredi, J.J., Rustgi, A.K. and Gu, W. (2023) Specific Regulation of BACH1 By the Hot Spot Mutant p53R175H Reveals a Distinct Gain of Function Mechanism. Nature Cancer. 4:564-581.

2022

Boni, N., Shapiro, L., Honig, B., Wu, Y. and Rubinstein, R. (2022) On the Formation of Ordered Protein Assemblies in Cell-cell Interfaces. Proc. Natl. Acad. of Sci.119:e2206175119 .

Xu, S., Sergeeva, A.P., Katsamba, P.S., Mannepalli, S., Bimela, J., Zipursky, S.L., Shapiro, L, Honig, B. and Zinn, Kai. (2022) Affinity Requirements for Control of Synaptic Targeting and Neuronal Cell Survival by Heterophilic IgSF Cell Adhesion Molecules. Cell Reports 39:110618.

Goodman, K.M., Katsamba, P.S., Rubinstein, R., Ahlsen, G., Bahna, F., Mannepalli, S., Dan, H., Sampogna, R.V., Shapiro, L. and Honig, B. (2022) How Clustered Protocadherin Binding Specifity is Tuned for Neuronal Self-/Nonself-Recognition. eLife 11:e72416.

2021

Blockus, H., Rolotti, S.V., Szoboszlay, M., Peze-Heidsieck, E., Ming, T., Schroeder, A., Apostolo, N., Vennekens, K.M., Katsamba, P.S., Bahna, F., Mannepalli, S., Ahlsen, G., Honig, B., Shapiro, L., de Wit, J., Losonczy, A. and Polleux, F. Synaptogenic Activity of the Axon Guidance Molecule Robo2 Underlies Hippocampal Circuit Function. Cell Reports 37:109828.

Troyanovsky, R.B., Sergeeva, A.P., Indra, I., Chen, C.-S., Kato, R., Shapiro, L., Honig, B. and Troyanovsky, S.M. (2021) Sorting of cadherin-catenin-associated proteins into individual clusters. Proc. Natl. Acad. of Sci. 118:e2105550118.

Murray, D., Petrey, D. and Honig, B. (2021) Integrating 3D Structural Information into Systems Biology. J. Biol. Chem. 296:100562.

Koss, H., Honig, B., Shapiro, L. and Palmer III, A.G. (2021) Cadherin-11 Dimerization Multi-site Kinetics: Combined Partial Unfolding and Strand-swapping. Structure 29:1105-1115.

Lasso, G., Honig, B. and Shapira, S. (2021) A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. Cell Systems. 12:82-91. Featured article.

Broyde, J., Simpson, D.R., Murray, D., Paull, E.O., Chu, B. W., Tagore, S., Jones, S.J., Griffin, A.T., Giorgi, F.M., Lachmann, A., Jackson, P., Sweet-Cordero, E.A., Honig, B. and Calfiano, A. (2021) Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nature Biotech. 39:215-224.

2020

Ganapathi, M., Argyriou, L., Martinez-Azorin, F., Morlot, S., Yigit, G., Lee, T.M., Auber, B., von Gise, A., Petrey, D.S., Thiele, H., Cyganek, L., Sabater-Molina, M, Ahimaz, P., Cabezas-Herrera, J., Sorli-Garcia, M., Zibat, A., Siegelin, M., Burfeind, P., Buchovecky, C.M., Hasenfuss, G., Honig, B., Li, Y., Iglesias,. A.D., Wollnik, B. (2020) Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenetics. Human Genetics 139:1443-1454.

Honig, B. and Shapiro, L. (2020) Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition. Cell 181:520-535.

Sergeeva, A.P., Katsamba, P.S., Cosmanescu, F., Brewer, J.J., Ahlsen, G., Mannepalli, S., Shapiro, L. and Honig B. (2020) DIP/Dpr Interactions and the Evolutionary Design of Specificity in Protein Families. Nature Comm. 11:2125.

Indra, I., Troyanovsky, R.B., Shapiro, L. Honig, B. and Troyanovsky, S.M. (2020) Sensing Actin Dynamics Through Adherens Junctions. Cell Reports 30:2820-2833.

Harrison, O.J., Brasch, J., Katsamba, P.S., Ahlsen, G., Noble, A.J., Dan, H., Sampogna, R.V., Potter, C.S., Carragher, B., Honig, B. and Shapiro, L. (2020) Family-wide Structural and Biophysical Analysis of Binding Interactions Among Non-clustered δ –Protocadherins. Cell Reports 30:2655-2671.

2019

Lasso, G., Mayer, S.V., Winkelmann, E.R., Chu, T., Elliot, O., Patino-Galindo, J.A., Park, K., Rabadan, R., Honig, B. and Shapira, S. (2019) A Structure Informed Atlas of Human-Virus Interactions. Cell 178:1526-1541.

Highlight - Singh, A., (2019) Human-Virus Interactome Atlas. Nature Methods 16:1081.

Generous, A.R., Harrison, O.J., Troyanovsky, R.B., Mateo, M., Navaratnarajah, C.K., Donohue, R.C., Pfaller, C.K., Alekhina, O., Sergeeva, A.P., Indra, I., Thornburg, T., Kochetkova, I., Billadeau, D.D., Taylor, M.P., Troyanovsky, S.M., Honig, B., Shapiro, L. and Cattaneo, R. (2019) Trans-endocytosis Elicited by Nectins Transfers Cytoplasmic Cargo Including Infectious Material Between Cells. J. Cell Sci. 132:jcs235507.

Brasch, J., Goodman, K.M., Noble, A.J., Rapp, M., Mannepalli, S., Bahna, F., Dandey, V.P., Bepler, T., Berger, B., Maniatis, T., Potter, C.S., Carragher, B., Honig, B. and Shapiro, L. (2019) Visualization of Clustered Protocadherin Neuronal Self-Recognition Complexes. Nature 569:280-283.

2018

Xu, S., Xiao, Q., Cosmanescu, F., Sergeeva, A.P., Yoo, J., Lin, Y., Katsamba, P.S., Ahlsen, G., Kaufman, J., Linavall, N., Lee, P.-T. Bellen, H., Shapiro, L., Honig, B. Tan, L. and Zipursky, S.L. (2018) Interactions Between the Ig-Superfamily Proteins DIP-α and Dpr6/10 Regulate Assembly of Neural Circuits. Neuron 100:1369-1384.

Cosmanescu, F., Katsamba, P.S., Sergeeva, A.P., Ahlsen, G., Patel, S.D., Brewer, J.J., Tan, L., Xu, S., Xiao, Q., Nagarkar-Jaiswal, S., Nern, A., Bellen, H., Zipursky, S.L., Honig, B. and Shapiro, L. (2018) Neuron Sub-type Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins. Neuron 100:1385-1400.

Yuan, L., Guo, L.-H., Yuan, C.-A., Zhang, Y.-H., Han, K., Nandi, A.-K., Honig, B. and Huang, D.-S. (2018) Integration of Multi-omics Data for Gene Regulatory Network Inference and Application to Breast Cancer. IEE/ACM Trans. Comput. Biol. Bioinform. 16:782-791.

Zeiske, T., Baburajendran, N., Kaczynska, A., Brasch, J., Palmer III, A.G., Shapiro, L., Honig, B. and Mann, R.S. (2018) Intrinsic DNA Shape Accounts for Affinity Differences Between HOX-Cofactor Binding Sites. Cell Reports 24:2221-2230.

Dionne, G., Qiu, X., Rapp, M., Liang, X., Zhao, B., Peng, G., Katsamba, P.S., Ahlsen, G., Rubinstein, R., Potter, C.S., Carragher, B., Honig, B., Müller, U. and Shapiro, L. (2018) Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture. Neuron 99:480-492.

Brasch, J., Katsamba, P.S., Harrison, O.J., Ahlsén, G., Troyanovsky, R., Indra, I., Kaczynska, A., Kaeser, B., Troyanovsky, S., Honig, B. and Shapiro, L. (2108) Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior. Cell Reports 23:1840-1852.

Indra, I., Choi, J., Chen, C.-S., Troyanvosky, R.B., Shapiro, L., Honig, B. and Troyanovsky, S.M. (2018) Spatial and Temporal Organization of Cadherin in Punctate Adherens Junctions. Proc. Natl. Acad. of Sci. 115:E4406-E4415.

Evangelista, F., Roth, A.J., Prisayanh, P., Temple, B.R., Li, N., Qian, Y., Culton, D.A., Liu, Z., Harrison, O.J., Brasch, J., Honig, B., Shapiro, L. and Diaz, L.A. (2018) Pathogenic IgG4 Autoantibodies from Endemic Pemphius Foliaceus Recognize a Desmoglein-1 Conformational Epitope. J. Autoimmun. 89:171-185.

2017

Hwang, H., Dey, F., Petrey, D. and Honig, B. (2017) Structure-based Prediction of Ligand-protein Interactions on a Genome-wide Scale. Proc. Natl. Acad. of Sci. 114:13685-13690.

Larsen, I.S.B., Narimatsu, Y., Joshi, H.J., Siukstaite, L., Harrison, O.J., Brasch, J., Goodman, K.M., Hansen, L., Shapiro, L., Honig, B., Vakhrushev, S.Y., Clausen, H. and Halim, A. (2017) Discovery of an O-Mannosylation Pathway Selectively Serving Cadherins and Protocadherins. Proc. Natl. Acad. of Sci. 114:11163-11168.

Chiu, T.-P., Rao, S., Mann, R.S., Honig, B. and Rohs, R., (2017) Genome-Wide Prediction of Minor-Groove Electrostatic Potential Enables Biophysical Modeling of Protein-DNA Binding. Nucl. Acid Res. 45:12565-12576.

Goodman, K.M., Rubinstein, R., Dan, H., Bahna, F., Mannepalli, S., Ahlsen, G., Thu, C.A., Sampogna, R.V., Maniatis, T., Honig, B. and Shapiro, L. (2017) Protocadherin cis-dimer Architecture and Recognition Unit Diversity. Proc. Natl. Acad. of Sci. 114:E9829-E9837.

Rubinstein, R., Goodman, K.M., Maniatis, T., Shapiro, L. and Honig, B. (2017) Structural Origins of Clustered Protocadherin-Mediated Neuronal Barcoding. Semin. Cell Dev. Bio. 69:140-150.

Larsen, I.S.B., Narimatsu, Y., Joshi, H.J., Yang, Z., Harrison, O., Brasch, J., Shapiro, L., Honig, B., Vakhurshev, S.Y., Clausen, H. and Halim, A. (2017) Mammalian O-mannosylation of Cadherins and Plexins is Independent of Protein O-mannosyltransferases 1 and 2. J. Biol. Chem. 292:11586-11598.

Lopez-Rivera, E., Liu, Y.P., Capone, V.P., Anderson, B.R., Verbitsky, M., Otto, E.A., Yan, Z., Fasel, D.A., Vukojevic, K., Mitrotti, A., Deng, R., Racedo, S., Liu, Q., Werth, M., Westland, R., Makar, G.S., Bodria., M., Sampson, M.G., Gillies, C.E., Vega-Warner, V., Maiorana, M., Petrey, D., Honig, B., Salomon, R., Carpentier, W., Gaillard, D., Carrea, A., Gesualdo, L., Cusi, D., Scolari, F., van Wijk, J., Babic-Saraga, M., Saraga, M., Bielenska, A.L., Materna-Kiryluk, A., McDonald-McGinn, D.M., Crowley, T.B., Zaniew, M., Darlow, J.M., Puri, P., Barton, D., Gucev, Z., Hakonarson, H., Flogelova, H., Tasic, V., Allegri, L., Wong, C.S., Drummond, I.A., D’Agati, V., Imamoto, A., Barasch, J.M., Hildebrant, F., Kiryluk, K., Lifton, R.P., Morrow, B., Jeanpierre, C., Papaioannou, V.E., Ghiggeri, G.M., Gharavi, A.G., Katsanis, N. and Sanna-Cherchi, S. (2017) Genetic Drivers of Kidney Defects in the DiGeorge Syndrome. New England Journal of Medicine 376:742-754.

Deng, C., Lipstein, M.R., Scotto, L., Jirau Serrano, X.O., Mangone, M.A., Li, S., Vendome, J., Hao, Y., Xu, X., Deng, S.X., Realubit, R.B., Tatonetti, N.P., Karan, C., Lentzsch, S., Fruman, D.A., Honig, B., Landry, D.W. and O’Connor, O.A. (2017) Silencing c-My Translation as a Therapeutic Strategy Through Targeting PI3K Delta and CK1 Epsilon in Hematological Malignancies. Blood 129:88-99.

Clark, A.J., Gindin, T., Zhang, B., Wang, L., Abel, R., Murret, C.S., Xu, F., Bao, A., Lu, N.J., Zhou, T., Kwong, P.D., Shapiro, L., Honig, B. and Friesner, R.A. (2017) Free Energy Perturbation Calculation of Relative Binding Free Energy Between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. J. Mol. Biol. 429:930-947.

2016

Stockman, V.B., Ghamsari, L., Lasso, G., Honig, B., Shapira, S.D. and Wang, H.H. (2016) A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions. PLoS One 11:e0167617.

Garzon, J.I., Deng, L., Murray, D., Shapira, S., Petrey, D. and Honig, B. (2016) A Computational Interactome and Functional Annotation for the Human Proteome. eLife 5:e18715.

Goodman, K.M., Rubinstein, R., Thu, C.A., Mannepalli, S., Bahna, F., Ahlsen, G., Rittenhouse, C., Maniatis, T., Honig, B. and Shapiro, L. (2016) γ-Protocadherin Structural Diversity and Functional Implications. eLife 5:e20930.

Goodman, K.M., Yamagata, M., Jin, X., Mannepalli, S., Katsamba, P.S., Ahlsen, G., Sergeeva, A.P., Honig, B., Sanes, J.R. and Shapiro, L. (2016) Molecular Basis of Sidekick-Mediated Cell-Cell Adhesion and Specificity. eLife 5:e19058.

Wang, D., Kon, N., Lasso, G., Jiang, L., Leng, W., Zhu, W.-G., Qin, J., Honig, B. and Gu, W. (2016) Acetylation-regulated Interaction Between p53 and SET Reveals a Widespread Regulatory Mode. Nature 538:118-122.

Sheng, R., Jung, D.-J., Silkov, A., Kim, H., Singaram, I., Wang, Z.-G., Xin, Y., Kim, E., Park, M.-J., Thiagarajan-Rosenkranz, P., Smrt, S., Honig, B., Beak, K., Ryu, S., Lorieua, J., Kim, Y.-M. and Cho, W. (2016) Lipids Regulate LcK Activity Through Their Interactions with Lck SH2 Domain. J. Cell Biol. 291:17639-17650.

Harrison, O.J., Brasch, J., Lasso, G., Katsamba, P.S., Ahlsen, G., Honig, B. and Shapiro, L. (2016) Structural Basis of Adhesive Binding By Desmocollins and Desmogleins. Proc. Natl. Acad. of Sci. 113:7160-7165.

Westphalen, C.B., Takemoto, Y., Tanaka, T., Macchini, M., Jiang, Z., Renz, B.W., Chen, X., Ormanns, S., Nagar, K., Tailor, Y., May, R., Cho, Y., Asfaha, S., Worthley, D.L., Haykawa, Y., Urbanska, A.M., Quante, M., Reichert, M., Broyde, J., Subramanian, P.S., Remotti, H., Su, G.H., Rustgi, A.K., Friedman, R.A., Honig, B., Califano, A., Houchen, C.W., Olive, K.P., and Wang, T.C. (2016) Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis. Cell Stem Cell 18:441-455.

Goodman, K.M., Rubinstein, R., Thu, C.A., Bahna, F., Mannepalli, S., Ahlsén, G., Rittenhouse, C., Maniatis, T., Honig, B. and Shapiro, L. (2016) Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins. Neuron 90:709-723.

Park, M.-J., Sheng, R., Silkov, A., Jung, D.-J., Wang, Z.-G., Xin, Y., Kim, H., Thiagarajan-Rosenkranz, P., Song, S., Yoon, Y., Wonhee, N., Kim, I., Kim, E., Lee, D.-G., Chen, Y., Singaram, I., Wang, L., Jang, M.H., Hwang, C.-S., Honig, B, Ryu, S., Lorieau, J., Kim, Y.-M. and Cho, W. (2016) SH2 Domains Serve As Lipid Binding Modules For pTyr-Signaling Proteins. Mol. Cell 62:7-20.

Hwang, H., Petrey, D. and Honig, B. (2016) A Hybrid Method for Protein-Protein Interface Prediction. Prot. Sci. 25:159-165.

2015

Barrows, D., Schoenfeld, S.M., Hodakoski, C., Silkov, A., Honig, B., Couvillon, A., Shymanets, A., Nurnberg, B., Asara, J.M. and Parsons, R. (2015) p21-activated Kinases (PAKs) Mediate the Phosphorylation of PREX2 to Initiate Feedback Inhibition of Rac1. J. Cell Biol. 290:28915-28931.

Rubinstein, R., Thu, C.A., Goodman,K.M., Wolcott, H.N., Bahna, F., Mannepalli, S., Ahlsen, G., Chevee, M., Halim, A., Clausen, H., Maniatis, T., Shapiro, L. and Honig, B. (2015) Molecular Logic of Neuronal Self-recognition Through Protocadherin Domain Interactions. Cell 163:629-642.

Biswas, K.H., Hartman, K.L., Yu, C.-H., Harrison, O., Song, H., Smith, A.W., Huang, W.Y.C., Lin, W.-C., Gou, Z., Padmanabhan, A., Troyanovsky, S.M., Dustin, M.L., Shapiro, L., Honig, B., Zaidel-Bar, R. and Groves, J.T. (2015) E-cadherin Junction Formation Involves an Active Kinetic Nucleation Process. Proc. Natl. Acad. of Sci. 112:10932-10937.

Chen, C.-S., Hong, S., Indra, I., Sergeeva, A., Troyanovsky, R., Shapiro, L., Honig, B. and Troyanovsky, S. (2015) α-Catenin-mediated Cadherin Clustering Couples Cadherin and Actin Dynamics. J. Cell Biol. 210:647-661.

Chen, T.S., Petrey, D., Garzon, J.I. and Honig, B. (2015) Predicting Peptide-Mediated Interactions on a Genome-Wide Scale. PLoS Comput. Biol. 11:e1004248.

Petrey, D., Chen, T.S., Deng, L., Garzon, J.I., Hwang, H., Lasso, G., Lee, H., Silkov, A. and Honig, B. (2015) Template-based Prediction of Protein Function. Curr. Op. Struc. Biol. 32:33-38.

2014

Kim, D.H., Park, M.-J., Gwon, G.H., Silkov, A., Xu, Z.-Y., Yang, E.C., Song, S., Song, K., Kim, Y., Yoon, H.S., Honig, B., Cho, W. and Cho, Y. (2014) An Ankyrin Repeat Domain of AKR2 Drives Chloroplast Targeting Through Coincident Binding of Two Chloroplast Lipids. Dev. Cell 30:598-609.

Vendome, J., Felsovalyi, K., Song, H., Yang, Z., Jin, X., Brasch, J., Harrison, O.J., Ahlsen, G., Bahna, F., Kaczynska, A., Katsamba, P.S., Edmond, D., Hubbell, W.L., Shapiro, L. and Honig, B. (2014) Structural and Energetic Determinants of Adhesive Binding Specificity in Type I Cadherins. Proc. Natl. Acad. of Sci. Plus 111:E4175-E4184.

Thu, C.A., Chen, W.V., Rubinstein, R., Chevee, M., Wolcott, H.N., Felsovalyi, K.O., Tapia, J.C., Shapiro, L., Honig, B. and Maniatis, T. (2014) Single-Cell Identity Generated by Combinatorial Homophilic Interactions Between α, β and γ Protocadherins. Cell 158:1045-1059.

Petrey, D. and Honig, B. (2014) Structural Bioinformatics of the Interactome. Ann. Rev. Biophysics 43:193-210.

Shazman, S., Lee, H., Socol, Y., Mann, R. and Honig, B. (2014) OnTheFly: A Database of Drosophila melanogaster Transcription Factors and Their Binding Sites. Nucl. Acid Res. 42: D167-D171.

2013

Li, Y., Altorelli, N.L., Bahna, F., Honig, B., Shapiro, L. and Palmer, A.G. 3rd (2013) Mechanism of E-Cadherin Dimerization Probed by NMR Relaxation Dispersion. Proc. Natl. Acad. of Sci. 110: 16462-16467.

Wu, Y., Honig, B. and Ben-Shaul, A. (2013) Theory and Simulations of Adhesion Receptor Dimerization on Membrane Surfaces. Biophys. J. 104:1221-1229.

Dey, F., Zhang, Q.C., Petrey, D. and Honig, B. (2013) Towards a “Structural BLAST”: Using Structural Relationships to Infer Function. Prot. Sci. 22:359-366.

Zhang, Q.C., Petrey, D., Garzon, J.I., Deng, L. and Honig, B. (2013) PrePPI: A Structure-Informed Database of Protein-Protein Interactions. Nucl. Acid Res. 41:D828-833.

2012

Harrison, O.J., Vendome, J., Brasch, J., Jin, X., Hong, S., Katsamba, P.S., Ahlsen, G., Troyanovsky, R.B., Troyanovsky, S.M., Honig, B. and Shapiro, L. (2012) Nectin Ectodomain Structures Reveal a Canonical Adhesive Interface. Nature Struc. Mol. Biol. 19:906-915.

Zhang, Q.C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C.A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., Maniatis, T., Califano, A. and Honig, B. (2012) Structure-based Prediction of Protein-protein Interactions on a Genome-wide Scale. Nature 490:556 - 560.

Brasch, J., Harrison, O.J., Honig, B and Shapiro, L. (2012) Thinking Outside the Cell: How Cadherins Drive Adhesion. Trends Cell Biol. 22:299-310.

Chen, Y., Sheng, R., Kallberg, M., Silkov, A., Tun, M.P., Bhardwaj, N., Kurilova, S., Hall, R.A., Honig, B., Lu, H. and Cho, W. (2012) Genome-Wide Identification and Functional Annotation of Dual Specificity Protein- and Lipid-Binding Modules that Moderate Protein Interactions at the Membrane. Mol. Cell 46:226-237.

Eletsky, A., Petrey, D., Zhang, Q.C., Lee, H.W., Acton, T.B., Xiao, R., Everett, J.K., Prestegard, J.H., Honig, B., Montelione, G.T. and Szyperski, T. (2012) Solution NMR Structures Reveal Unique Homodimer Formation by a Winged Helix-Turn-Helix Motif and Provide First Structures for Protein Domain Family PF10771. J. Struct Funct Genomics 13:1-7.

Floratos, A., Honig, B., Pe’er, D. and Califano, A. (2012) Using Systems and Structure Biology Tools to Dissect Cellular Phenotypes. J. Amer. Med. Inform. Assoc. 19:171-175.

Jin, X., Walker, M.A., Felsovalyi, K., Vendome, J., Bahna, F., Mannepalli, S., Cosmanescu, F., Ahlsen, G., Honig, B. and Shapiro, L. (2012) Crystal Structures of Drosophila N-cadherin Ectodomain Regions Reveal a Widely Used Class of Ca2+-free Interdomain Linkers. Proc. Natl. Acad. of Sci. 108:10133-10138.

2011

Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J. and Mann, R.S. (2011) Cofactor Binding Evokes Latent Differences in DNA Binding Specificity Between Hox Proteins. Cell 147:1270-1282.

Highlight - Ansari, A. and Peterson-Kaufman, K.J. (2011) A Partner Evokes Latent Differences Between Hox Proteins. Cell 147:1220.

Highlight - Stower, H. (2011) Gene Regulation: Resolving Transcription Factor Binding. Nature Rev. Genet. 13:71.

Bishop, E.P., Rohs,R., Parker, S.C., West, S.M., Liu, P., Mann, R.S., Honig, B. and Tullius, T.D. (2011) A Map of Minor Groove Shape and Electrostatic Potential From Hydroxyl Radical Cleavage Patterns of DNA. ACS Chem Biol. 6:1314-1320.

Kuziemko, A., Honig, B. and Petrey, D. (2011) Using Structure to Explore the Sequence Alignment Space of Remote Homologs. PLoS Comput. Biol. 10:e1002175.

Zhu, J., Yu, Y., Ulbrich, M.H., Li, M.-H., Isacoff, E.Y., Honig, B.H. and Yang, J. (2011) Structural Model of the TRPP2/PKD1 C-terminal Coiled-coil Complex Produced by a Combined Computational and Experimental Approach. Proc. Natl. Acad. of Sci. 108:10133-10138.

Zhang, Q.Z., Deng, L., Fischer, M., Guan, J., Honig, B. and Petrey, D. (2011) PredUs: A Web Server for Predicting Protein Interfaces Using Structural Neighbors. Nucl. Acid Res. 39:W283-W287.

Wu, Y., Vendome, J., Shapiro, L., Ben-Shaul, A. and Honig, B. (2011) Transforming Binding Affinities from Three Dimensions to Two With Application to Cadherin Clustering. Nature 475:510-513.

Vendome, J., Posy, S., Jin, X., Bahna, F., Ahlsen, G., Shapiro, L. and Honig, B. (2011) Molecular Design Principles Underlying β-strand Strand Swapping in the Adhesive Dimerization of Classical Cadherins. Nature Struc. Mol. Biol. 18:693-700.

Fischer, M., Honig, B. and Petrey, D. (2011) MarkUs: A Server to Navigate Sequence-Structure-Function Space. Nucl. Acid Res. 39:W357-W361.

Honig, B. and Rohs, R. (2011) Biophyics: Flipping Watson and Crick. Nature 470:472-473.

Harrison, O.J., Jin, X., Hong, S., Bahna, F., Ahlsen, G., Brasch, J., Wu, Y., Vendome, J., Felsovalyi, K., Hampton, C.M., Troyanovsky, R.B., Ben-Shaul, A., Troyanovsky, S.M., Shapiro, L. and Honig, B. (2011) The Extracellular Architecture of Adherens Junctions Revealed By Crystal Structures of Type I Cadherins. Structure 19:244-256.

Brasch, J., Harrison, O.J., Ahlsen, G., Carnally, S.M., Henderson, R.M., Honig, B. and Shapiro, L. (2011) Structure and Binding Mechanism of Vascular Endothelial Cadherin: A Divergent Classical Cadherin. J. Mol. Biol. 408:57-73.

Behnke-Parks, W.M., Vendome, J., Honig, B., Maliga, Z., Moores, C. and Rosenfeld, S.S. (2011) Loop L5 Acts As a Conformational Latch in the Mitotic Kinesin Eg5. J. Biol. Chem. 286:5242-5253.

2010

Love, J., Mancia, F., Shapiro, L, Punta, M., Rost, B., Girvin, M., Wang, D.N., Zhou, M., Hunt, J.F., Szperski, T., Gouaux, E., MacKinnon, R., McDermott, A., Honig, B., Inouye, M., Montelione, G. and Hendrickson, W.A. (2010) The New York Constorium on Membrane Protein Sturcture (NYCOMPS): A High-Throughput Platform for Structural Genomics of Integral Membrane Proteins. J. Struc. Func. Genomics 11:191-199.

Chen, B.Y. and Honig, B. (2010) VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity. PLoS Comput. Biol. 6:e1000881.

Wu, Y., Jin, X., Harrison, O., Shapiro, L., Honig, B. and Ben-Shaul, A. (2010) Cooperativity Between trans and cis Interactions in Cadherin-Mediated Junction Formation. Proc. Natl. Acad. of Sci. 107:17592-17597.

Koehnke, J., Katsamba, P.S., Ahlsen, G., Bahna, F., Vendome, J., Honig, B., Shapiro, L. and Jin, X. (2010) Splice Form Dependence of β-Neurexin/Neuroligin Binding Interactions. Neuron 67:61-74.

Highlight - Wei, Z. and Zhang, M. (2010) A Structural Approach to Decipher the Neurexin and Neuroligin Splice Isoform Code. Neuron 67:1-2.

Norel, R., Petrey, D. and Honig, B. (2010) PUDGE: A Flexible, Interactive Server for Protein Structure Prediction. Nucl. Acid Res. 38:W550-554.

Zhang, Q.C., Petrey, D., Norel, R. and Honig, B. (2010) Protein Interface Conservation Across Structure Space. Proc. Natl. Acad. of Sci. 107:10896-10901.

Lee, H., Li, Z., Silkov, A., Fischer, M., Petrey, D., Honig, B., and Murray, D. (2010) High-Throughput Computational Structure-Based Characterization of Protein Families: START Domains and Implications for Structural Genomics. J. Struc. and Func. Genomics 11:51-59.

Kitayner, M., Rozenberg, H., Rohs, R., Suad, O., Rabinovich, D., Honig, B. and Shakked, Z. (2010) Diversity in DNA Recognition by P53 Revealed by Crystal Structures with Hoogsteen Base Pairs. Nature Struc. Mol. Biol. 17:423-429.

Highlight - Chitayat, S. and Arrowsmith, C.H. (2010) Four p(53)s in a Pod. Nature Struc. Mol. Biol. 17:390-391.

Rohs, R., Jin, X., West, S.M., Joshi, R., Honig, B. and Mann, R.S. (2010) Origins of Specificity in Protein-DNA Recognition. Ann. Rev. Biochem. 79:233-269.

Singarapu, K.K., Mills, J.L., Xiao, R., Acton, T., Punta, M., Fisher, M., Honig, B., Rost, B., Montelione, G.T., Szyperski, T. (2010) Solution NMR Structures of Proteins VPA0419 from Vibrio parahaemolyticus and yiiS form Shigella flexneri Provide Structural Coverage for Protein Domain Family PFAM 04175. Proteins: Struct. Func. Bioinform. 78:779-784.

Harrison, O.J., Bahna, F., Katsamba, P.S., Jin, X., Brasch, J., Vendome, J., Ahlsen, G., Carroll, K.J., Price, S.R., Honig, B. and Shapiro, L. (2010) Two-Step Adhesive Binding by Classical Cadherins. Nature Struc. Mol. Biol. 17:348-358.

Ciatto, C., Bahna, F., Zampieri, N., Vansteenhouse, H.C., Katsamba, P.S., Ahlsen, G., Harrison, O.J., Brasch, J., Jin, X., Posy, S., Vendome, J., Ranscht, B., Jessell, T.M., Honig, B. and Shapiro, L. (2010) T-cadherin Structures Reveal a Novel Adhesive Binding Mechanism. Nature Struc. Mol. Biol. 17:339-347.

Cheng, L., Zhu, J., Hui, W.H., Zhang, X., Honig, B., Fang, Q. and Zhou, Z.H. (2010) Backbone Model of an Aquareovirus Virion by Cryo-Electron Microscopy and Bioinformatics. J. Mol. Biol. 397:852-863.

Zhu, J., Cheng, L., Fang, Q., Zhou, H. and Honig, B. (2010) Building and Refining Protein Models within Cryo-electron Microscopy Density Maps Based on Homology Modeling and Multiscale Structure Refinement. J. Mol. Biol. 397:835-851.

West, S.M., Rohs, R., Mann, R.S. and Honig B. (2010) Electrostatic Interactions Between Arginines and the Minor Groove in the Nucleosome. J. Biomol. Struct & Dynamics 27:861-866.

2009

Petrey, D. and Honig, B. (2009) Is Protein Classification Necessary? Towards Alternate Approaches to Funtion Annotation. Curr. Opin. Struc. Biol. 19:363-368.

Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack Jr., R.L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek Jr., S.R., Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D. and Wilson, I.A. (2009) Outcome of a Workshop on Applications of Protein Models in Biomedical Research. Structure 17:151-159.

Rohs, R., West, S.M., Liu, P. and Honig, B. (2009) Nuance in the Double-Helix and its Role in Protein-DNA Recognition. Curr. Opin. Struc. Biol. 19:171-177.

Katsamba, P., Carroll, K., Ahlsen, G., Bahna, F., Vendome, J., Posy, S., Rajebhosale, M., Price, S., Jessell, T.M., Ben-Shaul, A., Shapiro, L. and Honig, B. (2009) Linking Molecular Affinity and Cellular Specificity in Cadherin-Mediated Adhesion. Proc. Natl. Acad. of Sci. 106:11594-11599.

Petrey, D., Fischer, M. and Honig, B. (2009) Structural Relationships Among Proteins With Different Global Topologies and Their Implications for Function Annotation Strategies. Proc. Natl. Acad. of Sci. 106:17377-17382.

Rossi, P., Aramini, J.M., Xiao, R., Chen, C.X., Nwosu, C., Owens, L.A., Maglaqui, M., Nair, R., Fischer, M., Acton, T.B., Honig, B., Rost, B., and Montelione, G.T. (2009) Structural Elucidation of the Cys-His-Glu-Asn Proteolytic Relay in the Secreted CHAP Domain Enzyme From the Human Pathogen Staphylococcus saprophyticus. Proteins: Struct. Func. Bioinform. 74:515-519.

Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The Role of DNA Shape in Protein-DNA Recognition. Nature 461:1248-1253.

Highlight - Tullis, T. (2009) Structural Biology: DNA Binding Shapes Up. Nature 461:1225-1226.

Highlight - HHMI Chronicle In Brief. (2010) Double Helix, Revised. HHMI Bulletin. Feb:40-41.

2008

Soto, C.S., Fasnacht, M., Zhu, J., Forrest, L. and Honig, B. (2008) Loop Modeling: Sampling, Filtering and Scoring. Proteins: Struct. Func. Bioinform. 70:834-843.

Koehnke, J., Jin, X., Budreck, E.C., Posy, S., Scheiffele, P., Honig, B. and Shapiro, L. (2008) Crystal Structure of the Extracellular Cholinsterase-Like Domain from Neuroligin-2. Proc. Natl. Acad. of Sci. 105:1873-1878.

Koehnke, J., Jin, X., Trbovic, N., Katsamba, P., Brasch, J., Ahlsen, G., Scheiffele, P., Honig, B., Palmer, A. and Shapiro, L. (2008) Crystal Structures of β-Neurexin 1 and β-Neurexin Ectodomains and Dynamics of Splice Insertion Sequence 4. Structure 16:410-421.

Zhu, J., Fan, H., Periole, X., Honig, B. and Mark, A. E. (2008) Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials. Proteins: Struct. Func. Bioinform. 72:1171-1188.

Posy, S., Shapiro, L. and Honig, B. (2008) Sequence and structure determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface? J. Mol. Biol. 378:952-966.

Forrest, L.R., Zhang, Y.-W., Jacobs, M.T., Gesmonde, J., Xie, L., Honig, B. and Rudnick, G. (2008) A Mechanism for Alternating Access in Neurotransmitter Transporters. Proc. Natl. Acad. of Sci. 105:10338-10343.

Highlight - Kanner, B.I. (2008) Structural Biology: It’s Not All in the Family. Nature 454:593-594.

Hightlight - Montoya, M. (2008) Accessible Transport. Nature Struc. Mol. Biol 15:785.

Miloushev, V., Bahna, F., Ciatto, C., Ahlsen, G., Honig, B., Shapiro, L. and Palmer, A.G. (2008) Dynamic Properties of a Type II Cadherin Adhesive Domain: Implications for the Mechanism of Strand-Swapping of Classical Cadherins. Structure 16:1195-1205.

Kosloff, M., Alexov, E., Arshavsky, V.Y. and Honig, B. (2008) Electrostatic and Lipid-Anchor Contributions to the Interaction of Transducin with Membranes. J. Biol. Chem. 283:31197-31207.

2007

Tang, C. L., Alexov, E., Pyle, A.M. and Honig, B. (2007) Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides. J. Mol. Biol. 366:1475-1496.

Siggers, T. W. and Honig, B. (2007) Structure-Based Prediction of C2H2 Zinc-Finger Binding Specificity: Sensitivity to Docking Geometry. Nucl. Acid Res. 35:1085-1097.

Bertonati, C., Honig, B. and Alexov, E. (2007) Poisson-Boltzmann Calculations of Non-Specific Salt Effects on Protein-Protein Binding Free Energies. Biophys. J. 92:1891-1899.

Sosinsky, A., Honig, B., Mann, R. S. and Califano, A. (2007) Discovering Transcriptional Regulatory Regions in Drosophila by a Non-Alignment Method for Phylogentic Footprinting. Proc. Natl. Acad. of Sci. 104:6305-6310.

Xiang, Z., Steinbach, P.J., Jacobson, M.P., Friesner, R.A. and Honig, B. (2007) Prediction of Side-Chain Conformations on Protein Surfaces. Proteins: Struct. Func. Bioinform. 66:814-823.

Singarapu, K.K., Liu, G., Xiao, R., Bertonati, C., Honig, B, Montelione, G. and Szyperski, T. (2007) NMR Structure of Protein yjbR From Escherichia coli Reveals ‘Double-wing’ DNA Binding Motif. Proteins: Struct. Func. Bioinform. 67:501-504.

Fasnacht, M., Zhu, J. and Honig, B. (2007) Local Quality Assessment in Homology Models Using Statistical Potentials and Support Vector Machines. Prot. Sci. 16:1557-1568.

Honig, B. (2007) Protein Structure Space is Much More Than the Sum of it Folds. Nature Struc. and Mol. Biol. 14:458.

Forrest, L., Tavoulari, S., Zhang, Y.-W., Rudnick, G. and Honig, B. (2007) Identification of a Chloride Ion Binding Site in Na+/Cl--dependent Transporters. Proc. Natl. Acad. of Sci. 104:12761-12766.

Highlight - Chin, G. (2007) Biochemistry Studying Ions in Depth. Science 317:873.

Highlight - Amara, S. (2007) Chloride Finds Its Place in the Transport Cycle. Nature Struc. and Mol. Biol. 14:792-794.

Joshi, R., Passner, J.M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M.A., Jacob, V., Aggarwal, A.K., Honig, B. and Mann, R.S.  (2007) Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure. Cell 131:530-543.

Highlight - Harrison, S.C. (2007) Three-dimensional Intricacies in Protein-DNA Recognition and Transcriptional Control. Nature Struc. and Mol. Biol. 14:1118-1119.

Highlight - Zomot, E. (2007) A Cotransporter Family Takes (-) Charge. Cell 130:963.

Highlight - Leading Edge. Exd Gets Hox into the Groove. Cell 131:421.

Shapiro, L. and Honig, B. (2007) Cell - to - Cell Contact and Extracellular Matrix. Curr. Opin. Cell Biol. 19:493-494.

2006

Nayal, M. and Honig, B. (2006) On the Nature of Cavities on Protein Surfaces: Application to the Identification of Drug Binding Sites. Proteins: Struct. Funct. Bioinform. 63:892-906.

Patel, S.D., Ciatto, C., Chen, C.P., Bahna, F., Rajebhosale, M., Arkus, N., Schieren, I., Jessell, T.M., Honig, B., Price, S.R. and Shapiro, L. (2006) Type II Cadherin Ectodomain Structures: Implications for Classical Cadherin Specificity. Cell 124:1255-1268.

Ortiz, C.O., Etchberger, J.F., Posy, S.L., Forkjaer-Jensen, C., Lockery, S., Honig, B. and Hobert, O.  (2006) Searching for Neuronal Left/Right Asymmetry: Genome Wide Analysis of Nematode Receptor-Type Guanylyl Cyclases. Genetics 3:131-149.

Zhu, J., Xie, L. and Honig, B. (2006) Structural Refinement of Protein Segments Containing Secondary Structure Elements: Local Sampling, Knowledge-Based Potentials and Clustering. Proteins: Struct. Func. Bioinform. 65:463-479.

Forrest, L. R., Tang, C.L., and Honig, B. (2006) On the Accuracy of Homology Modeling and Alignment Methods Applied to Membrane Proteins. Biophys. J. 91:508-517.

Kolodny, R, Petrey, D. and Honig, B. (2006) Protein Structure Comparison: Implications for the Nature of ‘Fold Space’, and Structure and Function Prediction. Curr. Opin. Struc. Biol. 16:393-398.

Kolodny, R and Honig, B. (2006) VISTAL – A New 2D Visualization Tool of Protein 3D Structural Alignments. Bioinformatics 22:2166-2167.

Lin, Y.-C., Liu, G., Shen, Y., Bertonati, C., Yee, A., Honig, B., Arrowsmith, C. and Szyperski. T. (2006) NMR Structure of Protein PA2021 From Pseudomonas aeruginosa. Proteins: Struct. Func. Bioinform. 65:767-770.

Johnston, Jr., R. J., Copeland, J.W., Fasnacht, M., Etchberger, J.F., Liu, J., Honig, B. and Hobert, O. (2006) An Unusual Zn-Finger/FH2 Domain Protein Controls a Left/Right Asymmetric Neuronal Fate Decision in C. elegans. Development 133:3317-3328.

2005

Siggers, T., Silkov, A and Honig, B. (2005) Structural Alignment of Protein-DNA Interfaces: Insights into the Determinants of Binding Specificity. J. Mol. Biol. 345: 1027-1045.

Fan, H., Mark, A. E., Zhu, J. and Honig, B. (2005) Comparative Study of Generalized Born Models: Protein Dynamics. Proc. Natl. Acad. of Sci. 102:6760-6764.

Zhu, J., Alexov, E. and Honig, B. (2005) Comparative Study of Generalized Born Models: Born Radii and Peptide Folding. J. Phys. Chem. 109:3008-3022.

Murray, D and Honig, B. (2005) To B or Not to B: PIP2 Answers the Question. Dev. Cell 8:138-9.

Shen, Y., Goldsmith-Fischman, S., Atreya, H. S., Acton, T., Ma, L., Xiao, R., Honig, B., Montelione and G. T. Szyperski, T. (2005) NMR Structure of the 18 kDa Protein CC1736 From Caulobacter Crescentus Identifies a Member of the “START” Domain Superfamily and Suggests Residues Mediating Substrate Specificity. Proteins: Struc., Func. and Bioinform. 58:747-750.

Wildonger, J., Sosinsky, A., Honig, B. and Mann, R. S. (2005) Lozenge Directly Activates Argos and Klumpfuss to regulate Programmed Cell Death. Genes and Dev. 19:1034-1039.

Forrest, L. R. and Honig, B. (2005) An Assessment of the Accuracy of the Methods for Predicting Hydrogen Positions in Protein Structures. Proteins: Struct. Funct. Bioinform. 61:296-309.

Chen, C. P., Posy, S., Ben-Shaul, A., Shapiro, L. and Honig, B. (2005) Specificity of Cell-Cell Adhesion by Classical Cadherins: Critical Role for Low-Affinity Dimerization Through β-strand Swapping. Proc. Natl. Acad. Sci. 102:8531-8536.

Siggers, T., Silkov, A. and Honig, B. (2005) Bending in the Right Direction. Structure 13:1400-1401.

Petrey, D. and Honig, B.  (2005) Protein Structure Prediction: Inroads to Biology. Mol. Cell 20:811-819.

Murray, P. S., Li, Z., Wang, J., Tang, C. L., Honig, B. and Murray, D. (2005) Retroviral Matrix Domains Share Electrostatic Homology: Models for Membrane Binding Function Throughout the Viral Life Cycle. Structure 13:1521-1531.

Powers, R., Mirkovic, N., Goldsmith-Fischman, S., Acton, T.B., Chiang, Y., Huang, Y.J., Ma, L., Rajan, P.K., Cort, J.R., Kennedy, M.A., Liu, J., Rost, B., Honig, B., Murray, D. and Montelione, G. (2005) Solution Structure of Archaeglobus fulgidis Peptidly-tRNA Hydrolase (Pth2) Provides Evidence for an Extensive Conserved Family of Pth2 Enzymes in Archea, Bacteria, and Eukaryotes. Prot. Sci. 14:2849-2861.

2004

Jacobson, M.P., D.L. Pincus, C.S. Rapp, T.J.F. Day, B. Honig, D.E. Shaw, and R.A. Friesner. (2004) A hierarchical approach to all-atom loop prediction. Proteins: Struct. Funct. Bioinform. 55:351-367.

Xu, D., Liu, G. Xiao, R., Acton, T., Goldsmith-Fischman, S., Honig, B., Montelione, G. and Szyperski, T. (2004) NMR Structure of the Hypothetical Protein AQ-1857 Encoded by the Y157 Gene From Aquifex aeolicus Reveals a Novel Protein Fold. Proteins: Struc. Func. Bioinform. 54:794-796.

Liu, G., Sukumaran, D. K., Xu, D., Chiang, Y., Acton T, Goldsmith-Fischman, S., Honig, B., Montelione, G. T., and Szyperski, T. (2004) NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins: Struct. Func. Bioinform. 55:756-758.

Goldsmith-Fischman, S., Kuzin, A., Edstrom, W. C.,  Benach, J., Shastry, R.,  Xiao, R., Acton, T. B., Honig, B., Montelione, G. T., and Hunt, J. F. (2004) The SufE Sulfur-Acceptor Protein Contains a Conserved Core Structure that Mediates Interdomain Interactions in a Variety of Redox Protein Complexes. J. Mol. Biol. 344:549-565.

Ramelot, T. A., Cort, J. R., Goldsmith-Fischman, S., Kornhaber, G. J., Xiao, R., Shastry, R., Acton, T. B., Honig, B., Montelione, G. T., and Kennedy, M. A. (2004) Solution structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. J. Mol. Biol. 344:567-583.

Fleishman, S. J., Harrington, S., Friesner, R. A., Honig, B. and Ben-Tal, N. (2004) An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-EM and Evolutionary Data. Biophys. J. 87:3448-3459.

Gimpelev, M., Forrest, L. R., Murray, D and Honig, B. (2004) Helical Packing Patterns in Membrane and Soluble Proteins. Biophys. J. 87: 4075-4086.

2003

Alexov, E. and Honig, B. (2003) Structural and Energetic Basis of Molecular Recognition in Handbook of Cell Signaling, R. Bradshaw and E. A. Dennis, Editors, Academic Press, San Diego, CA. p.11-13.

Petrey, D., Xiang, Z., Tang, C. L., Xie, L., Gimpelev, M., Mitros, T., Soto, C. S., Goldsmith-Fischman, S., Kernytsky, A., Schlessinger, A., Koh, I. Y. Y., Alexov, E. and Honig, B. (2003) Using Multiple Structure Alignments, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling. Proteins: Struc., Func. and Genet. 53:430-435.

Sosinsky, A., Bonin, K., Mann, R. S. and Honig, B. (2003) Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acid Res. 31:3598-3592.

Goldsmith-Fischman, S. and Honig, B. (2003) Structural Genomics: Computational Methods for Structure Analysis. Prot. Sci. 12:1813-1821.

Tao, X., Khayat, R., Christendat, D., Savchenko, A., Xu, X., Goldsmith-Fischman, S., Honig, B., Edwards, A., Arrowsmith, C. and Tong, L. (2003) Crystal Structures of MTH1187 and Its Yeast Ortholog YBL001c. Proteins: Struc., Func. and Genet. 52:478-480.

Ramelot, T. A., Ni, S., Goldsmith-Fischman, S., Cort, J. R., Honig, B. and Kennedy, M. A. (2003) Solution Structure of Vibrio Cholerae Protein VC0424: A Variation of the Ferredoxin-Like Fold. Protein Sci. 12:1556-1561.

Petrey, D. and Honig, B. (2003) GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences. Methods in Enzymology 374, 492-509.

Sheinerman, F. B., Al-Lazikani, B. and Honig, B. (2003) Sequence, Structure and Energetic Determinants of Phosphopeptide Selectivity of SH2 Domains. J. Mol. Biol. 334:823-841.

Tang, C. L., Xie, L., Koh, I. Y. Y., Posy, S., Alexov, E. and Honig, B. (2003) On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles. J. Mol. Biol. 334:1043-1062.

Patel, S. D., Chen, C. P., Bahna, F., Honig, B. and Shapiro, L. (2003) Cadherin-Mediated Cell-Cell Adhesion: Sticking Together as a Family. Curr. Op. Struc. Biol. 13:690-698.

Aramini, J. M., Huang, Y. J., Cort, J. R., Goldsmith-Fischman, S., Xiao, R., Shih, L.-Y., Ho, C. K., Lui, J., Rost, B., Honig, B., Kennedy, M. A., Acton, T. B. and Montelione, G. T.  (2003) Solution NMR Structure of the 30S Ribosomal Protein S28E From Pyrococcus horikoshii. Prot. Sci. 12:2823-2830.

2002

Murray, D. and Honig, B. (2002) Electrostatic Control of the Membrane Targeting of C2 Domains. Mol. Cell 9:145-154.

Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A. and Honig, B. (2002) Rapid Grid-Based Construction of the Molecular Surface and the Use of Induced Surface Charge to Calculate Reaction Field Energies: Applications to the Molecular Systems and Geometric Objects. J. Comp.  Chem. 23:128-137.

Sheinerman, F. and Honig, B. (2002) On the Role of Electrostatic Interactions in the Design of Protein-Protein Interfaces. J. Mol. Biol. 318:161-177.

Xiang, Z., Soto, C. and Honig, B. (2002) Evaluating Conformational Free Energies: The Colony Energy and its Application to the Problem of Loop Prediction. Proc. Natl. Acad. Sci. USA 99:7432-7437.

Murray, D., Arbuzova, A., Honig, B. and McLaughlin, S. (2002) The Role of Electrostatic and Nonpolar Interactions in the Association of Peripheral Proteins with Membranes. Curr. Topics in Membranes 52:277-307.

Jacobson, M. P., Friesner, R. A., Xiang, Z. and Honig, B. (2002) On the Role of the Crystal Environment in Determining Protein Side Chain Conformations. J. Mol. Biol. 320:597-608.

Rost, B., Honig, B. and Valencia, A. (2002) Bioinformatics in Structural Genomics. Bioinformatics 18:897-898.

2001

Al-Lazikani, B., Jung, J., Xiang, Z., and Honig, B. (2001) Protein Structure Prediction. Curr. Opinion in Chem. Biol. 5:51-56.

Gerstein, M. and Honig, B. (2001) Sequences and Topology. Curr. Opinion in Struc. Biol. 11:327-329.

Norel, R., Sheinerman, F., Petrey, D. and Honig, B. (2001) Electrostatics Contributions to Protein-Protein Interactions: Fast Energetic Filters for Docking and Their Physical Basis.  Prot. Sci. 10:2147-2161.

Xiang, Z. and Honig, B. (2001) Extending the Accuracy Limits of Prediction for Side Chain Conformations. J. Mol. Biol. 311:421-430.

Rocchia, W., Alexov, E. and Honig, B. (2001) Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions. J. Phys. Chem. B. 105:6507-6514.

Murray, D., McLaughlin, S. and Honig, B. (2001) The Role of Electrostatic Interactions in the Regulation of the Membrane Association of G Protein βγ Heterodimers. J. Biol. Chem. 276:45153-45159.

Al-Lazikani, B., Sheinerman, F. and Honig, B. (2001) Combining Multiple Structure and Sequence Alignments to Improve Sequence Detection and Alignment: Application to the SH2 Domains of Janus Kinases. Proc. Natl. Acad. Sci. USA 98:14796-14801.

2000

Sheinerman, F., Norel, R. and Honig, B. (2000) Electrostatic Aspects of Protein-protein Interactions. Curr. Opinion in Struc. Biol. 10:153-159.

Yang, A.-S. and Honig, B. (2000) An Integrated Approach to the Analysis of Sequence and Structure. I. Protein Structural Alignment and a Quantitative Measure for Protein Structural Distance. J. Mol. Biol. 301: 665-678.

Yang, A.-S. and Honig, B. (2000) An Integrated Approach to the Analysis of Sequence and Structure. II. On the Relationship Between Sequence and Structural Similarity for Proteins that are not Obviously Related in Sequence. J. Mol. Biol. 301: 679-689.

Yang, A.-S. and Honig, B. (2000) An Integrated Approach to the Analysis of Sequence and Structure. III. A Comparative Study of Sequence Conservation in Protein Structural Families Using Multiple Structural Alignments. J. Mol. Biol. 301: 691-711.

Arbuzova, A., Wang, L., Wang, J., Hangyás-Mihályné, G., Murray, D., Honig, B. and McLaughlin, S. (2000) Membrane Binding of Peptides Containing Both Basic and Aromatic Residues. Experimental Studies with Peptides Corresponding to the Scaffolding Region of Caveolin and the Effector Region of MARCKS. Biochemistry 39: 10330-10339.

Ben-Tal, N., Honig, B., Bagdassarian, C. K. and Ben-Shaul, A. (2000) Association Entropy in Adsorption Processes. Biophys. J. 79:1180-1187.

Petrey, D. and Honig, B. (2000) Free Energy Determinants of Tertiary Structure and the Evaluation of Protein Models. Protein Science 9:2181-2191.

1999

Nayal, M., Hitz, B.C., and Honig, B. (1999) GRASS: A Server for the Graphical Representation and Analysis of Structures. Prot. Sci. 8:676-679.

Xiao, L. and Honig, B. (1999) Electrostatic Contributions to the Stability of Hyperthermophilic Proteins. J. Mol. Biol. 289:1435-1444.

Nielsen, J. E., Andersen, K. V., Honig, B., Hooft R. W. W., Klebe, G., Vriend, G., and Wade, R. C. (1999) Improving Macromolecular Electrostatics Calculations. Protein Eng. 12: 657-662.

Yang, A.-S. and Honig, B. (1999) Sequence to Structure Alignment in Comparative Modeling using PrISM. Proteins: Struc., Func. and Genet. Suppl.3:66-72.

Honig, B. (1999) Protein Folding: From the Levinthal Paradox to Structure Prediction. J. Mol. Biol. 293:283-293.

Chin, K., Sharp, K., Honig, B. and Pyle, A. M. (1999) Calculating the Electrostatic Properties of RNA Provides New Insights Into Molecular Interactions and Function. Nature Struct. Biol. 6:1055-1061.

Polticelli, F., Ascenzi, P., Bolgonesi, M. and Honig, B. (1999) Structural Determinants of Trypsin Affinity and Specificity for Cationic Inhibitors. Prot. Sci. 8:2621-2629.

Murray, D., Arbuzova, A., Mihaly, G., Gambir, A., Ben-Tal, N., Honig, B. and McLaughlin, S. (1999) Electrostatic Properties of Membranes Containing Acidic Lipids and Adsorbed Basic Peptides: Theory and Experiment. Biophys. J. 77:3176-3188.

1998

Murray, D., Hermida-Matsumoto, L., Buser, C.A., Tsang, J., Sigal, C.T., Ben-Tal, N., Honig, B., Resh, M.D., and McLaughlin, S. (1998) Electrostatics and the Membrane Association of Src: Theory and Experiment. Biochemistry 37:2145-2159.

Misra, V., Hecht, J., Yang, A.-S., and Honig, B. (1998) Electrostatic Contributions to the Binding Free Energy of the λcI Repressor to DNA. Biophys. J. 75:2262-2273.

1997

Ben-Tal, N., Sitkoff, D., Topol, I.A., Yang, A.-S., Burt, S.K., and Honig, B. (1997) Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution. J. Phys. Chem. B. 101:450-457.

Froloff, N., Windemuth, A., and Honig, B. (1997) On the Calculation of Binding Free Energies Using Continuum Methods: Application to MHC Class I Protein-Peptide Interactions. Prot. Sci. 6:1293-1301.

Ben-Tal, N., Honig, B., Miller, C., and McLaughlin, S. (1997) Electrostatic Binding of Proteins to Membranes. Theoretical Predictions and Experimental Results with Charybdotoxin and Phospholipid Vesicles. Biophys. J. 73:1717-1727.

Chen, S-w W. and Honig, B. (1997) Monovalent and Divalent Salt Effects on Electrostatic Free Energies Defined by the Nonlinear Poisson-Boltzmann Equation: Application to DNA Reactions. J. Phys. Chem. B. 101:9113-9118.

Murray, D., Ben-Tal, N., Honig, B., and McLauglin, S. (1997) Electrostatic Interaction of Myristolyated Proteins with Membranes: Simple Physics, Complicated Biology. Structure 5:985-989.

Honig, B.  (1997) New Challenges in Computational Biochemistry. Pacific Symposium on Biocomputing 21:21-24.

1996

Sitkoff, D., Ben-Tal, N., and Honig, B. (1996) Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models. J. Phys. Chem. 100:2744-2752.

Misra, V.K.  and Honig, B. (1996) The Electrostatic Contribution to the B to Z Transition of DNA. Biochem. 35:1115-1123.

Ben-Tal, N., Ben-Shaul, A., Nicholls, A., and Honig, B. (1996) Free-Energy Determinants of α-Helix Insertion into Lipid Bilayers. Biophys. J. 70:1803-1812.

Ben-Shaul, A., Ben-Tal, N., and Honig, B. (1996) Statistical Thermodynamic Analysis of Protein Insertion into Lipid Membranes. Biophys. J. 71:130-137.

Yang, A.-S., Hitz, B., and Honig, B. (1996) Free Energy Determinants of Secondary Structure Formation: III. β Turns and their Role in Protein Folding. J. Mol. Biol. 259:873-882.

Sampogna, R.V. and Honig, B. (1996) Electrostatic Coupling Between Retinal Isomerization and the Ionization State of Glu-204: A General Mechanism for Proton Release in Bacteriorhodopsin. Biophys. J. 71:1165-1171.

Gunner, M.R., Nicholls, A., and Honig, B. (1996) Electrostatic Potentials in Rhodopseudomonas viridis Reaction Centers: Implications for the Driving Force and Directionality of Electron Transfer. J. Phys. Chem. 100:4277-4291.

Lancaster, C.R.D., Michel, H., Honig, B., and Gunner, M.R. (1996) Calculated Coupling of Electron and Proton Transfer in the Photosynthetic Reaction Center of Rhodpseudomonas viridis. Biophys. J. 70:2469-2492.

Honig, B. and Cohen, F. (1996) Adding Backbone to Protein Folding: Why proteins are polypeptides. Folding & Design 1:R17-R20.

Marten, B., Kim, K., Cortis, C., Friesner, R.A., Murphy, R.B., Ringnalda, M.N., Sitkoff, D. and Honig, B. (1996) New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen-Bonding Effects. J. Phys. Chem. 100:11775-11788.

Sharp., K. A., Kumar, S., Rossky, P. J., Friedman, R.A. and Honig, B. (1996) Size Dependence of Transfer Free Energies. 2 Hard Sphere Models. J. Phys. Chem. 100:14166-14177.

Ben-Tal, N., Honig, B., Peltzsch, R. M., Denisov, G., and McLaughlin, S. (1996) Binding of Small Basic Peptides to Membranes Containing Acidic Lipids: Theoretical Models and Experimental Results. Biophys. J. 71:561-575.

Friedman, R.A.and Honig, B. (1996) Response to S.H. Gellman, T.S. Haque, and L.F. Newcomb. Biophys. J. 71:3525-3526.

Ben-Tal, N. and Honig, B. (1996) Helix-Helix Interactions in Lipid Bilayers. Biophys J. 71:3046-3050.

1995

Misra, V.K. and Honig, B. (1995) On the Magnitude of the Electrostatic Contribution to Ligand-DNA Interactions. Proc. Natl. Acad. Sci. USA 92:4691-4695.

Kumar, S.K., Szleiffer., I., Sharp, K.A., Rossky, P., Friedman, R., Honig, B. (1995) Size Dependence of Transfer Free Energies 1. A Flory-Huggins Approach. J. Phys. Chem. 99:8382-8391.

Honig, B. and Yang, A.-S. (1995) Free Energy Balance in Protein Folding. Advances in Protein Chemistry 46:27-58.

Bharadwaj, R., Windemuth, A., Sridharan, S., Honig, B., Nicholls, A. (1995) The Fast Multipole Boundary Element Method for Molecular Electrostatics: An Optimal Approach for Large Systems. J. Comp. Chem. 16:898-913.

Hecht, J.L., Honig, B., Shin, Y.-K., Hubbell, W.L. (1995) Electrostatic Potentials Near the Surface of DNA: Comparing Theory and Experiment. J. Phys. Chem. 99: 7782-7786.

Sharp,. K.A., Friedman, R.A., Misra, V., Hecht, J., Honig, B. (1995) Salt Effects on Polyelectrolyte-Ligand Binding: Comparison of Poisson-Boltzmann, and Limiting/Law Counterion Binding Models. Biopolymers 36:245-262.

Vorobjev, Y.N. Scheraga, H.A., Honig, B. (1995) Theoretical Modeling of the Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in Polar Ionic Solution. 2. pH-Induced Helix-Coil Transition of Poly (l-lysine) in Water and Methanol Ionic Solutions. J. Phys. Chem. 99:7180-7187.

Honig, B. and Nicholls, A. (1995) Classical Electrostatics in Biology and Chemistry. Science 268:1144-1149.

Friedman, R.A.and Hong, B. (1995) A Free Energy Analysis of Nucleic Acid Base Stacking in Aqueous Solution. Biophys. J. 69:1528-1535.

Sharp, K.A. and Honig, B. (1995) Salt Effects on Nucleic Acids. Curr. Opinion in Struc. Biol. 5:323-328.

Yang, A.-S. and Honig, B. (1995) Free Energy Determinants of Secondary Structure Formation: I. α-Helices. J. Mol. Biol. 252:351-365.

Yang, A.-S. and Honig, B. (1995) Free Energy Determinants of Secondary Structure Formation: II. Antiparallel β-Sheets. J. Mol. Biol. 252:366-376.

Honig, B., Ottolenghi, M., and Sheves, M. (1995) Acid-Base Equilibria and the Proton Pump in Bacteriorhodospin. Israel J. Chem. 35:429-446.

1994

Smith, K.S. and Honig, B. (1994) Evaluation of the Conformational Free Energies of Loops in Proteins. Proteins: Struc., Func. and Genet.:18:119-132.

Monge, A., Freisner, R. and Honig, B. (1994) An Algorithm to Generate Low Resolution Protein Tertiary Structures from Secondary Structure Assignments. Proc. Natl. Acad. Sci. USA 91:5027-5029.

Misra, V.K., Sharp, K.A. , Friedman, R.A., and Honig, B. (1994) Salt Effects on Ligand-DNA Binding. Minor Groove Binding Antibiotics. J. Mol. Biol. 238:245-263.

Misra, V.A., Hecht, J.L., Sharp, K.A., Friedman, R.A. and Honig, B. (1994) Salt Effects on Protein-DNA Interactions. The λcI Repressor and EcoRI Endonuclease. J. Mol. Biol. 238:264-280.

Sitkoff, D., Sharp, K.A., and Honig, B. (1994) Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 98:1978-1988.

Yang, A. and Honig, B. (1994) Structural Origins of pH and Ionic Strength Effects on Protein Stability: Acid Denaturation of Sperm Whale Apomyoglobin. J. Mol. Biol. 237:602-614.

Scott, D.L., Mandel, A.M., Sigler, P.B. and Honig, B. (1994) The Electrostatic Basis for the Interfacial Binding of Secretory Phospholipases A2. Biophys. J. 67:493-504.

Sitkoff, D., Lockhardt., D.J., Sharp, K.A., Honig, B. (1994) Calculation of Electrostatic Effects at the Amino Terminus of an α-helix. Biophys. J. 67:2251-2260.

Sitkoff, D., Sharp, K.A., and Honig, B. (1994) Correlating Solvation Free Energies and Surface Tensions of Hydrocarbon Solutes. Biophys. Chem. 51:397-409.

Sampogna, R.V. and Honig, B. (1994) Environmental Effects on the Protonation States of Active Site Residues in Bacteriorhodopsin. Biophys. J. 66:1341-1352.

Tannor, D.J., Marten, B., Murphy, R., Friesner, R.A., Sitkoff, D., Nicholls, A., Ringnalda, M., Goddard III., W.A., and Honig, B. (1994) Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectic Theory. J. Am. Chem. Soc. 116:11875-11882.

Rajasekaran, E., Jayaram, B. and Honig, B. (1994) Electrostatic Interactions in Aliphatic Dicarboxylic Acids: A Computational Route to the determination of pKa shifts. J. Am. Chem. Soc. 116:8238-8240.

Vorobjev, Y.N., Scheraga, H.A., Hitz, B. and Honig, B. (1994) Theoretical Modeling of the Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in Polar Ionic Solution. I. Potential of Mean Force Between Charged Lysine Residues and Titration of Poly(L-lysine) in 95% Methanol Solution. J. Phys. Chem. 98:10940-10948.

1993

Yang, A.-S., Gunner, M.R., Sampogna, R., Sharp, K.A. and Honig, B. (1993) On the Calculation of pKas in Proteins. Proteins: Struc., Func. and Genet. 15:252-265.

Yang, A.-S. and Honig, B. (1993) On the pH Dependence of Protein Stability. J. Mol. Biol. 231:459-474.

Honig, B., Sharp, K.A. and Yang, A.-S. (1993) Macroscopic Models of Aqueous Solutions:  Biological and Chemical Applications. J. Phys. Chem. 97:1101-1109.

Tanzi, R.E., Petrukhin, K., Chernov, I., Pellequer, J.L., Wasco, W., Ross, B., Romano, D.M., Parano, E., Brzustowicz, L.M., Devoto, M., Peppercorn, J., Bush, A.I., Sternlieb, I., Pirastu, M., Gusella, J.F., Evgrafov, O., Penchaszadeh, G.K., Honig, B., Edelman, I.S, Soares, M.B., Scheinberg, I.H. and Gilliam, T.C. (1993) The Wilson Disease Gene is a Copper Transporting ATPase with Homology to the Menkes' Disease Gene. Nature Genetics 5:344-350.

1992

Friedman, R.A. and Honig, B. (1992) The Electrostatic Contribution to DNA Base-Stacking Interactions. Biopolymers 32:145-159.

McGrath, M.E., Vasquez, J.R., Craik, C.S., Yang, A.S., Honig, B., and Fletterick, R.J. (1992) Perturbing the Polar Environment of Asp102 in Trypsin: Consequences of Replacing Conserved Ser214. Biochem. 31:3059-3064.

Sharp, K., Jean-Charles, A., and Honig, B. (1992) A Local Dielectric Constant Model for Solvation Free Energies Which Accounts for Solute Polarizability. J. Phys. Chem. 96:3822-3828.

Yang, A.-S. and Honig, B. (1992) Electrostatic effects on protein stability. Curr. Opinion in Struc. Biol. 2:40-45.

Yang, A.-S, Sharp, K.A. and Honig, B. (1992) Analysis of the Heat Capacity Dependence of Protein Folding. J. Mol. Biol. 227:889-890.

Gunner, M. and Honig, B. (1992) Calculations of Proton Uptake in Rhodobacter Sphaeroides Reaction Centers. The Photosynthetic Bacterial Reaction Centre:  Structure, Spectroscopy, and Dynamic, J. Breton and Dr. Vermeglio, Editors, Plenum Publishing Company Ltd., England, p.403-410.

1991

Gilson, M.K. and Honig, B. (1991) The Inclusion of Electrostatic Hydration Energies in Molecular Mechanics Calculations. J. Comp. Aided Molecular Design 5:5-20.

Gunner, M.R. and Honig, B. (1991) Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center. Proc. Natl. Acad. Sci. USA. 88:9151-9155.

Honig, B. (1991) In Memoriam: Cyrus Levinthal. Proteins: Struc., Func. and Genet. 11:239-241.

Jean-Charles, A., Nicholls, A., Sharp, K., Honig, B., Tempczyk, A., Hendrickson, T.F. and Still, W.C. (1991) Electrostatic Contributions to Solvation Energies: Comparison of Free Energy Perturbation and Continuum Calculations. J. Am. Chem. Soc. 113:1454-1455.

Nicholls, A. and Honig, B. (1991) A Rapid Finite Difference Alogrithm, Utililizing Successive Over-Relaxation to Solve the Poisson-Boltzman Equation. J. Comp. Chem. 12:435-445.

Sharp, K.A., Nicholls, A., Fine, R., and Honig, B. (1991)  Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic Effects. Science 252:106-109.

Honig, B. (1991) Theory and simulation: Editorial overview. Curr. Opinion in Struct. Biol. 1:169-170.

Sharp, K.A., Nicholls, A. , Friedman, R. and Honig, B. (1991) Extracting Hydrophobic Free Energies from Experimental Data: Relationship to Protein Folding and Theoretical Models. Biochem. 30:9686-9697.

Nicholls, A. Sharp, K.A. and Honig, B. (1991) Protein Folding and Association:  Insights From the Interfacial and Thermodynamic Properties of Hydrocarbons. Proteins: Struc., Func. and Genet. 11:281-296.

1990

Sharp, K., Honig, B. and Harvey, S. (1990) Electrical Potential of Transfer RNAs: Codon-Anticodon Recognition. Biochem. 29:340-346.

Gunner, M. and Honig, B. (1990) Electrostatic Analysis of the Midpoints of the Four Hemes in the Bound Cytochrome of the Reaction Center of Rp. Viridis., Perspectives in Photosynthesis. J. Jortner and B. Pullman, Editors, Kluwer Academic Publishers, Netherlands, pp. 53-60.

Honig, B. (1990) Environmental Effects on Electrostatic Interactions. Theoretical Biochemistry & Molecular Biophysics Volume 2: Proteins, David L. Beveridge and Richard Lavery, Editors, Adenine Press,  pp. 63-67.

Jayaram, B., Swaminathan, S., Beveridge, D., Sharp, K., and Honig, B. (1990) Monte Carlo Simulation Studies on the Structure of the Counterion of B-DNA. Variations on the Primitive Dielectric Model. Macromolecules 23:3156-3165.

Koutalos, Y., Ebrey, T.G., Gilson, H.R., and Honig, B. (1990) Octopus Photoreceptor Membranes.  Surface Charge Density and pK of the Schiff Base of the Pigments. Biophys. J. 58:493-501.

Sharp, K. and Honig, B. (1990) Electrostatic Interactions in Macromolecules: Theory and Applications. Ann. Rev. Biophys. Biophys. Chem. 19:301-332.

Sharp, K.A. and Honig, B. (1990) Calculating Total Electrostatic Energies with the Nonlinear Poisson-Boltzmann Equation. J Phys. Chem. 94:7684-7692.

Sharp, K. and Honig, B. (1990) Applications of the Finite Defference Poisson-Boltzman Method to Proteins and Nucleic Acids. Structure and Methods, Vol 2: DNA Protein Complexes & Proteins. Ed. Ramaswamy H. Sarma and Mukti H. Sarma, Adenine Press. p211-214.

1989

Jayaram, B., Fine, R., Sharp, K.A. and Honig, B. (1989) Free Energy Calculations of Ion Hydration: An Analysis of the Born Model in Terms of Microscopic Simulations. J. Phys. Chem. 93:4320-4327.

Jayaram, B., Sharp, K.A. and Honig, B. (1989) The Electrostatic Potential of B-DNA. Biopolymers 28:975-993.

Honig, B., Sharp, K. and Gilson, M. (1989) Electrostatic Interactions in Proteins.  Computer Assisted Modeling of Receptor Ligand Interactions: Theoretical Aspects and Applications to DNA Design, R. Rein and A. Golombek, Editors, Alan R. Liss, Inc., New York, p. 65-74.

Gilson, M. and Honig, B. (1989) Destabilization of an α-Helical Bundle by Helix Dipoles. Proc. Natl. Acad. Sci. USA 86:1524-1528.

Koutalos, Y., Ebrey, T.G., Tsuda, M., Odashima, K., Lien, T., Park, M.H., Shimizu, N., Derguini, F., Nakanishi, K., Gilson, H. and Honig, B. (1989) Regeneration of Bovine and Octopus Opsins in Situ with Natural  and Artificial Retinals. Biochem. 28:2732-2739.

Chen, J.G., Nakamura, T., Ebrey, T.G., Ok, H., Konno, K., Derguini, F., Nakanishi, K. and Honig, B. (1989) Wavelength Regulation in Iodopsin, a Cone Pigment. Biophys. J. 55:725-729.

Soman, K., Yang, A.-S., Honig, B. and Fletterick, R. (1989) Electrical Potentials in Trypsin Isozymes. Biochem. 28:9918-9926.

Sharp, K. and Honig, B. (1989) Lattice models of Electrostatic Interaction:  The Finite Difference Poisson-Boltzmann Method. Chemica Scripta 29A:71-74.

1988

Gilson, M., Sharp K. and Honig, B. (1988) Calculation of  the Total Electrostatic Energy of a Macromolecular System: Solvation Energies, Binding Energies, and Conformational Analysis. Proteins: Struc., Func. and Genet. 4:7-18.

Gilson, M.K. and Honig, B.H. (1988) Energetics of Charge-Charge Interactions in Proteins. Proteins: Struc., Func, and Genet. 3:32-52.

Gilson, H., Honig, B., Croteau, A., Zarrilli, G. and Nakanishi, K. (1988) Analysis of the Factors Which Influence the C=N Stretching Frequency of Polyene Schiff Bases:  Implications for Bacteriorrhodopsin and Rhodopsin. Biophys. J. 53:261-269.

Eccles, J., Honig, B. and Schulten, K. (1988) Spectroscopic Determinants in the Reaction Center of Rhodopseudomonas viridis. Biophys. J. 53:137-144.

Gilson, H. and Honig, B.H. (1988) Analysis of NMR and Absorption Spectroscopic Data in Bacteriorhodopsin:  Models for Protein Chromophore Interactions. J. Am Chem. Soc. 110:1943-1950.

Lanyi, J., Zimanyi, L., Nakanishi, K., Derguini, F., Okabe, M. and Honig, B. (1988) Chromophore/Protein and Chromosphore/Anion Interactions in Halorhodopsin. Biophys. J. 53:185-191.

1987

Sharp, K., Fine, R., Schulten, K. and Honig, B. (1987) Brownian Dynamics Simulations of Diffusion to Irregular Bodies. J. Phys. Chem. 91:3624-3631.

Sharp, K., Fine, R. and Honig, B. (1987) Computer Simulations of the Diffusion of a Substrate to an Active Site of an Enzyme. Science 236:1460-1463.

Gilson, M. and Honig, B. (1987) Calculation of Electrostatic Potentials in an Enzyme Active Site. Nature 330:84-86.

Honig, B. (1987) External Point Charges and Amino Sequence in Retinal Proteins. Biophysical Studies of Retinal Proteins. K. Nakanishi, T. Ebrey, B. Honig and H. Frauenfelder, Editors, University of Illinois Press, Urbana, IL p. 212-218.

Sharp, K., Gilson, M., Fine, R. and Honig, B. (1987) Electrostatic Interactions in Proteins.  Protein Structure, Folding and Design 2, (UCLA Symposia on Mol. Cell. Biol.) Alan R. Liss, Inc.,  2:235-244.

Gilson, M., Sharp, K.A. and Honig, B. (1987) Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment. J. Comp. Chem. 9:327-335.

1986

Rashin, A. A., Iofin, M. and Honig, B. (1986) Interval Cavities and Buried Waters in Globular Proteins. Biochem. 25:3619-3623.

Honig, B., Hubbell, W.L. and Flewelling, R.F. (1986) Electrostatic Interactions in Membranes and Proteins. Ann. Rev. Biophys. Biophys. Chem. 15:163-169.

Gilson, M. and Honig, B. (1986) The Dielectric Constant of a Folded Protein. Biopolymers 25:2097-2119.

Spudich, J.L., McCain, D.A., Nakanishi, K., Okabe, M., Shimizu, N., Rodman, H., Honig, B. and Bogomolni, R.A. (1986) Chromophore/Protein Interaction in Bacterial Sensory Rhodopsin and Bacteriorhodopsin. Biophys. J. 49:479-483.

Klapper, I., Hagstrom, R., Fine, R., Sharp, K. and Honig, B. (1986) Focusing of Electric Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and Amino-Acid Modification. Proteins: Struc., Func. and Genet. 1:47-59.

1985

Kakitani, H., Kakitani, T., Rodman, H. and Honig, B. (1985) On the Mechanism of Wavelength Regulation in Visual Pigments. Photochem. Photobiol. 41:471-479.

Rashin, A.A. and Honig, B. (1985) Reevaluation of the Born Model of Ion Hydration. J. Phys. Chem. 89:5588-5593.

Gilson, M., Rashin, A., Fine, R. and Honig, B. (1985) On the Calculation of Electrostatic Interactions in Proteins. J. Mol. Biol. 184:503-516.

Schiffmiller, R., Callender, R., Waddell, W., Govindjee, R., Ebrey, T., Kakitani, H., Honig, B. and Nakanishi, K. (1985) Resonance Raman Studies of Bacteriorhodopsin Analogues. Photochem. Photobiol. 41:563-567.

1984

Honig, B. (1984) Electrostatic Interactions in Membrane Proteins.  Information and Energy Transduction in Biological Membranes: Proceedings of the International Conference on Biological Membranes, Held in Crans-Sur-Si, L.C. Bolis and E.J. Helmreich, Editors, Alan R. Liss, N.Y., N.Y., p 149-152.

Rashin, A. and Honig, B. (1984) On the Environment of Ionizable Groups in Globular Proteins. J. Mol. Biol. 173:515-521.

Honig, B. and Hubbell, W. (1984) Stability of “Salt-bridges” in Membrane Proteins. Proc. Natl. Acad. Sci. USA 81:5412-5416.

Doukas, A.G., Junnarkar, M.R., Alfano, R.R., Callender, R.H., Kakitani, H. and Honig, B. (1984) Fluorescene quantum yield of visual pigments: Evidence for Subpicosecond Isomerization Rates. Proc. Natl. Acad. Sci. USA 81:4790-4794.

1983

Eccles, J. and Honig, B. (1983) Charged Amino-Acids as Spectroscopic Determinants for Chlorophyll in vivo. Proc. Natl. Acad. Sci. USA 80:4959-4962.

Kakitani, T., Kakitani, H., Honig, B. and Nakanishi, K. (1983) Symmetric Charge Distribution in Bacteriorhodopsin Binding Site. J. Am. Chem. Soc. 105:648-650.

Kakitani, H., Kakitani, T., Rodman, H., Honig, B. and Callender, R. (1983) Correlation of Vibrational Frequencies with Absorption Maxima in Polyenes, Rhodopsin, Bacteriorhodopsin and Retinal Analogues. J. Phys. Chem. 87:3620-3628.

1982

Honig, B. (1982) Photochemical Charge Separation and Active Transport in the Purple Membrane. “Electrogenic Ion Pumps”, Current Topics in Membranes and Transport , C. Slayer, Editor, Academic Press, Inc. 16:371-386.

Honig, B. (1982) Theoretical Aspects of Photoisomerization in Visual Pigments and Bacteriorhodopsin. Biological Aspects of Ultrafast Laser Spectroscopy, R. Alfano, Editor, Academic Press, N.Y. p 57-63.

Kakitani, T., Honig, B., and Crofts, A.R. (1982) Theoretical Studies of the Electrochromic Response of Cartotenoids in Photosynthetic Membranes. Biophys. J. 39:57-63.

1981

Dinur, U., Honig, B. and Ottolenghi, M. (1981) Analysis of Primary Photochemcial Processes in Bacteriorhodopsin. Photochem. Photobiol. 33:523-527.

Honig, B. (1981) Excited State Properties of Visual Pigments and Bacteriorhodopsin.  Annal. N.Y. Acad. Sci. 376:269-280.

Kalisky, O., Ottolenghi, M., Honig, B. and Korenstein, R. (1981) Environmental Effects on the Formation and Photoreaction of the M412 Photoproduct of Bacteriorhodopsin: Implications for the Mechanism of Proton Pumping. Biochem. 20:649-655.

Doukas, A., Pande, A., Suzuki, T., Callender, R., Honig, B. and Ottolenghi, M. (1981) On the Mechanism of Hydrogen-Deuterium Exchange in Bacteriorhodopsin. Biophys. J. 33:275-280.

Balogh-Nair, V., Carriker, J.D., Honig, B., Ramat, V., Motto, M.G., Nakanishi, K., Sen, R., Sheves, M., Tanis, M.A. and Tsujimoto, K. (1981) The 'Opsin Shift' in Bacteriorhodopsin:  Studies with Artificial Bacteriorhodopsins. Photochem. Photobiol. 33:483-488.

1980

Aton, B., Doukas, A., Narva, D.,  Callender, R., Dinur, U. and Honig, B. (1980) Resonance Raman Studies of the Primary Photochemical Event in Visual Pigments. Biophys. J. 29:79-94.

Dinur, U. and Honig, B. (1980) A Consistent Semiempirical Theory for the Calculation of Ground and Excited State Properties. J. Chem. Phys. 72:1817-1829.

Dinur, U., Honig, B. and Schulten, K. (1980) On the Nature of Excited Electronic States in Cyanine Dyes: Implications for Visual Pigment Spectra. Chem. Phys. Lett. 72:493-497.

Schulten, K., Dinur, U. and Honig, B. (1980) The Spectra of Carbonium Ions, Cyanine Dyes, and Protonated Schiff Base Polyenes. J. Chem. Phys. 73:3927-3935.

Nakanishi, K., Balogh-Nair, V., Arnaboldi, M., Tsujimoto, K. and Honig, B. (1980) An External Point Charge Model for Bacteriorhodopsin to Account for its Purple Color. J. Am. Chem. Soc. 102:7945-7947.

Honig, B., Dinur, U., Birge, R., and Ebrey, T.G. (1980) The Isomer Dependence of Oscillator Strengths in Retinal and Related Molecules. Spectroscopic Assignments. J. Am. Chem. Soc. 102:488-494.

1979

Nakanishi, K., Balogh-Nair, V., Gawinowicz, M.A., Arnaboldi, M., Motto, M., Honig, B. (1979) Double Point Charge Model for Visual Pigments: Evidence From Dihydrorhodopsins. Photochem. Photobio. 29:657-660.

Dinur, U. and Honig, B. (1979) On the Effects of Methyl Substitution on the Exited States of Butadiene.  J. Am. Chem. Soc.101:4453-4460.

Dinur, U. and Honig, B. (1979) Natural Orbitals of s-cis-Butadiene and Their Relation to Photochemical Cyclization. Chem. Phys. Lett. 64:588-592.

Honig, B., Ebrey, T., Callender, R.H., Dinur, U., and Ottolenghi, M. (1979) Photoisomerization, energy storage, and charge separation: A model for light energy transduction in visual pigments and bacteriorhodopsin. Proc. Natl. Acad. Sci. USA 76:2503-2507.

Honig, B., Dinur, U., Nakanishi, K., Balogh-Nair, V., Gawinowicz, M.A., Arnaboldi, M, and Motto, M. (1979) An External Point-Charge Model for Wavelength Regulation in Visual Pigments. J. Am. Chem. Soc.101:7084-7086.

Sheves, M., Nakanishi, K. and Honig, B. (1979) Through Space Electrostatic Effects in Electronic Spectra. Experimental Evidence for the External Point Charge Model of Visual Pigments. J. Am. Chem. Soc. 101:7086-7088.

1978

Hagler, A. and Honig, B. (1978) On the Formation of Protein Tertiary Structure on a Computer. Proc. Natl. Acad. Sci. USA 75:554-558.

Honig, B. (1978) Light Energy Transduction in Visual Pigments and Bacteriorhodopsin. Ann. Rev. Phys. Chem. 29:31-57.

Honig, B. and Stein, W.D. (1978) Design Principles for Active Transport Systems. J. Theor. Biol. 75:299-305.

Doukas, A.G., Aton, B., Callender, R. and Honig, B. (1978) The Resonance Raman Excitation Profile of All-Trans Retinal: Theoretical Implications. Chem. Phys. Letts. 56:248-252.

Aton, B., Callender, R. and Honig, B. (1978) Photochemical Cis-Trans Isomerization of Bovine Rhodopsin at Liquid Helium Temperatures. Nature 273:784-786.

Honig, B. (1978) Kinetic and Molecular Models for Proton Pumping in Bacteriorhodopsin. Energetics and Structures of Halophilic Microorganisms, S.R. Caplan and M. Ginzburg, Editors, Elsevier/North-Holland Biomedical Press, 109-121.

Yonath, A., Podjarny, A., Honig, B., Traub, W., Sielecki, A., Herzberg, O. and Moult, J. (1978) Structural Analysis of Denaturant-Protein Interactions: Comparison Between the Effects of Bromoethanol and SDS on Denaturation and Renaturation of Triclinic Lysozyme. Biophys. Struct. Mech. 4:27-36.

1977

Ebrey, T. and Honig, B. (1977) New Wavelength Dependent Visual Pigment Nomograms. Vision Res. 17:147-151.

Hagler, A. and Honig, B. (1977) Theoretical Studies of Protein Folding. In: Peptides Proc. of Fifth American Peptide Symposium. M. Goodman and J. Meienhofer, Editors, Wiley, New York, p 280-283.

Rosenfeld, T., Honig, B., Ottolenghi, M., Hurley, J. and Ebrey, T. (1977) Cis-Trans Isomerization in the Photochemistry of Vision. Pure and Appl. Chem. 49:341-351.

Callender, R.H. and Honig, B. (1977) Resonance Raman Studies of Visual Pigments. Ann. Rev. Biophys. Bioeng. 6:33-55.

Stein, W. and Honig, B. (1977) Models for Active Transport of Cations--A Steady State Analysis. Mol. Cell. Biochem. 15:27-44.

Ebrey T., Becher, B., Mao, B., Kilbride, P. and Honig, B. (1977) Exciton Interactions and Chromophore Orientation in the Purple Membrane. J. Mol. Biol. 112:377-397.

Hurley, J., Ebrey, T., Honig, B. and Ottolenghi, M. (1977) Temperature and Wavelength Effects on the Photochemistry of Rhodopsin, Isorhodopsin, Bacteriorhodopsin and Their Photoproducts. Nature 270:540-542.

Yonath, A., Podjarny, A., Honig, B., Sielecki, A. and Traub, W. (1977) Crystallographic Studies of Protein Denaturation and Renaturation. 2 Sodium Dodecyl Sulfate Induced Structural Changes in Triclinic Lysozyme. Biochem. 16:1418-1424.

1976

Honig, B. and Greenberg, A. (1976) Chromophore Protein Interactions in Visual Pigments and Their Analogs. Environmental Effects on Molecular Structure and Properties, B. Pullman, Editors, D. Reidel Publishing Co., Dordecht-Holland, p. 355-362. 

Honig, B., Ray, A. and Levinthal, C. (1976) Conformational Flexibility and Protein Folding: Rigid structural fragments connected by flexible joints in subtilisin BPN. Proc. Natl. Acad. of Sci. 73:1974-1978.

Honig, B., Greenberg, A.D., Dinur, U., and Ebrey, T.G. (1976) Visual-Pigment Spectra: Implications of the Protonation of the Retinal Schiff Base. Biochem. 15:4593-4599.

1975

Honig, B., Warshel, A. and Karplus, M. (1975) Theoretical Studies of the Visual Chromophore. Accounts of Chem. Res. 8:92-100.

Alchalel, A., Honig, B., Ottolenghi, M. and Rosenfeld, T. (1975) Triplet Sensitized Cis-Trans Isomerization of Protonated Schiff Bases of Retinal Isomers. J. Am. Chem. Soc. 97:2161-2166.

Ebrey, T. and Honig, B. (1975) Molecular Aspects of Photoreceptor Function. Quart. Rev. Biophys. 8:129-184.

Ebrey, T., Govindjee, R., Honig, B., Pollock, E., Chan , W., Crouch, R., Yudd, A. and Nakanishi, K. (1975) Properties of Several Sterically Modified Retinal Analogs and their Photosensitive Pigments. Biochem. 14:3933-3941.

Greenberg, A., Honig, B.,  and Ebrey, T. (1975) Wavelengths Dependence of Bandwidths of Visual Pigment Spectra Nature 257:823-824.

1974

Honig, B. and Ebrey, T. (1974) The Structure and Spectra of the Chromophore of the Visual Pigments. Ann. Rev. Biophys. Bioeng. 3:151-177.

Chan, W., Nakanishi, K., Ebrey , T. and Honig, B. (1974) Properties of 14-Methylretinal, 13-Desmethyl-14-Methylretinal and Visual Pigments Formed Therefrom. J. Am. Chem. Soc. 96:3642-3644.

1973

Honig, B., Khan, P., and Ebrey T. (1973) Intrinsic Optical Activity of Retinal Isomers: Implications for the Circular Dichroism Spectrum of Rhodopsin. Biochem. 12:1637-1643.

Honig, B., Kabat, E., Katz, L., Levinthal, C. and Wu, T. (1973) Model-Building of Neurohypophyseal Hormones. J. Mol. Biol. 80:277-295.

1972

Ebrey, T. and Honig, B. (1972) Ultraviolet Chromophore Transitions in the Rhodopsin Spectrum. Proc. Natl. Acad. Sci. USA 69:1897-1899.

1971

Honig, B. and Karplus, M. (1971) Implications of Torsional Potential of Retinal Isomers for Visual Excitation. Nature 229:558-560.

Honig, B., Hudson, B., Sykes, B. and Karplus, M. (1971) Ring Orientation in Beta-ionone and Retinals. Proc. Natl. Acad. Sci. USA 68:1289-1293.

1970

Scharf, B. and Honig, B. (1970) Comments on Vibronic Intensity Borrowing. Chem. Phys. Lett. 7:132-136.

1964 - 1969

Turner, A.G., Honig, B., Parr, R.G. and Hoyland, J.R. (1964) Off-Center Hydrogen Atom Calculations. J. Chem. Phys. 40:3216-3220.

Bradley, D.F., Lifson, S. and Honig, B. (1964) Theory of Optical and Other Properties of Biopolymers: Applicability and Elimination of the First-Neighbor and Diople-Diople Approximations. Electronic Aspects of Biochemistry. Academic Press,  New York, p77-91.

Honig, B., Jortner, J. and Szoke, A. (1967) Theoretical Studies of Two Photon Absorption:  I. Molecular Benzene. J. Chem. Phys. 46:2714-2727.

Honig, B. and Jortner, J. (1967) Theoretical Studies of Two Photon Absorption:  II. Model Calculations. J. Chem. Phys. 47:3698-3703.