Publications

2017

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. Accepted.

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. Mammalian O-mannosylation of Cadherins and Plexins is Independent of Protein O-mannosyltransferases 1 and 2. J. Biol. Chem. 292:11586-11598.

Deng C, Lipstein MR, Scotto L, Jirau Serrano XO, Mangone MA, Li S, Vendome J, Hao Y, Xu X, Deng SX, Realubit RB, Tatonetti NP, Karan C, Lentzsch S, Fruman DA, Honig B, Landry DW, O'Connor OA. Silencing c-Myc translation as a therapeutic strategy through targeting PI3K delta and CK1 epsilon in hematological malignancies. Blood (2017) 129:88-99.

Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA. Free energy perturbation calculation of relative binding free energy between broadly neutralizing antibodies and the gp120 glycoprotein of HIV-1. J. Mol. Biol.  (2017) 429:930-47.

Lopez-Rivera E, Liu YP, Capone VP, Anderson BR, Verbitsky M, Otto EA, Yan Z, Fasel DA, Vukojevic K, Mitrotti A, Deng R, Racedo S, Liu Q, Werth M, Westland R, Makar GS, Bodria M, Sampson MG, Gillies CE, 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 AL, Materna-Kiryluk A, McDonald-McGinn DM, Crowley TB, Zaniew M, Darlow JM, Puri P, Barton D, Gucev Z, Hakonarson H, Flogelova H, Tasic V, Allegri L, Wong CS, Drummond IA, D’Agati V, Imamoto A, Barasch JM, Hildebrant F, Kiryluk K, Lifton RP, Morrow B, Jeanpierre C, Papaioannou VE, Ghiggeri GM, Gharavi AG, Katsanis N, Sanna-Cherchi S. Genetic dissection of the Renal Disease of DiGeorge Syndrome. New Engl. J. Med. (2017) 376:742-54.

2016

Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction. Protein Sci. (2016) 25:159-65.

Goodman KM, Rubinstein R, Thu CA, Bahna F, Mannepalli S, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. Structural basis of diverse homophilic recognition by clustered α- and β-protocadherins. Neuron (2016) 90:709-23.

Harrison OJ, Brasch J, Lasso G, Katsamba PS, Ahlsen G, Honig B, Shapiro L. Structural basis of adhesive binding by desmocollins and desmogleinsProc. Natl. Acad. Sci. USA (2016) 113:7160-5.

Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsén G, Sergeeva AP, Honig B, Sanes JR, Shapiro L. Molecular basis of sidekick-mediated cell-cell adhesion and specificity. Elife (2016) 5:e19058.

Goodman KM, Rubinstein R, Thu CA, Mannepalli S, Bahna F, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. γ-Protocadherin structural diversity and functional implications. Elife (2016) 5:e20930.

Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. A computational interactome and functional annotation for the human proteome. Elife (2016) 5:e18715. 

Park MJ, Sheng R, Silkov A, Jung DJ, Wang ZG, Xin Y, Kim H, Thiagarajan-Rosenkranz P, Song S, Yoon Y, Nam W, Kim I, Kim E, Lee DG, Chen Y, Singaram I, Wang L, Jang MH, Hwang CS, Honig B, Ryu S, Lorieau J, Kim YM, Cho W. SH2 domains serve as lipid binding modules for pTyr-signaling proteins. Mol. Cell (2016) 62:7-20.

Westphalen CB, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y, May R, Cho Y, Asfaha S, Worthley DL, Hayakawa Y, Urbanska AM, Quante M, Reichert M, Broyde J, Subramaniam PS, Remotti H, Su GH, Rustgi AK, Friedman RA, Honig B, Califano A, Houchen CW, Olive KP, Wang TC. Dclk1 defines quiescent pancreatic progenitors that promote injury-induced regeneration and tumorigenesis. Cell Stem Cell (2016) 18:441-55.

Sheng R, Jung D-J, Silkov A, Kim, H., Ingaram 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, Cho W. Lipids regulate LcK activity through their interactions with Lck SH2 domain. J. Biol. Chem. (2016) 291:17639-50.

Wang D, Kon N, Lasso G, Jiang L, Leng W, Zhu W-G, Qin J, Honig B, Gu W. Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory modeNature (2016) 538:118-22.

Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH. A high-throughput strategy for dissecting mammalian genetic interactions. PLoS One (2016) 11:e0167617. 

2015

Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A, Honig B. Template-based prediction of protein function. Curr. Opin. Struct. Biol. (2015) 32:33-8.

Chen TS, Petrey D, Garzon JI, Honig B. Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comput. Biol. (2015) 11:e10042

Chen CS, Hong S, Indra I, Sergeeva AP, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM. α-Catenin-mediated cadherin clustering couples cadherin and actin dynamics. J. Cell Biol. (2015) 210:647-61.

Biswas KH, Hartman KL, Yu CH, Harrison OJ, Song H, Smith AW, Huang WY, Lin WC, Guo Z, Padmanabhan A, Troyanovsky SM, Dustin ML, Shapiro L, Honig B, Zaidel-Bar R, Groves JT. E-cadherin junction formation involves an active kinetic nucleation process. Proc. Natl. Acad. Sci. USA (2015) 112:10932-7.

Rubinstein R, Thu CA, Goodman KM, Wolcott HN, Bahna F, Mannepalli S, Ahlsen G, Chevee M, Halim A, Clausen H, Maniatis T, Shapiro L, Honig B. Molecular logic of neuronal self-recognition through protocadherin domain interactions. Cell (2015) 163:629-42.

Barrows D, Schoenfeld SM, Hodakoski C, Silkov A, Honig B, Couvillon A, Shymanets A, Nürnberg B, Asara JM, Parsons R. p21-activated kinases (PAKs) mediate the phosphorylation of PREX2 to initiate feedback inhibition of Rac1. J. Biol. Chem. (2015) 290:28915-31.

2014

Shazman S, Lee H, Socol Y, Mann RS, Honig B. OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res. (2014)            42(Database issue):D167-71.

Petrey D, Honig B. Structural bioinformatics of the interactome. Ann. Rev. Biophys. (2014) 43:193-210.

Thu CA, Chen WV, Rubinstein R, Chevee M, Wolcott HN, Felsovalyi KO, Tapia JC, Shapiro L, Honig B, Maniatis T. Single-cell identity generated by combinatorial homophilic interactions between α, β, and γ protocadherins. Cell (2014) 158:1045-59. 

Vendome J, Felsovalyi K, Song H, Yang Z, Jin X, Brasch J, Harrison OJ, Ahlsen G, Bahna F, Kaczynska A, Katsamba PS, Edmond D, Hubbell WL, Shapiro L, Honig B. Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proc. Natl. Acad. Sci. USA (2014) 111:E4175-84.

Kim DH, Park MJ, Gwon GH, Silkov A, Xu ZY, Yang EC, Song S, Song K, Kim Y, Yoon HS, Honig B, Cho W, Cho Y, Hwang I. An ankyrin repeat domain of AKR2 drives chloroplast targeting through coincident binding of two chloroplast lipids. Dev. Cell (2014) 30:598-609.

2013

Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. (2013) 41(Database issue):D828-33.

Dey F, Cliff Zhang Q, Petrey D, Honig B. Toward a "structural BLAST": using structural relationships to infer function. Protein Sci. (2013) 22:359-66.

Wu Y, Honig B, Ben-Shaul A. Theory and simulations of adhesion receptor dimerization on membrane surfaces. Biophys. J. (2013) 104:1221-9. 

Li Y, Altorelli NL, Bahna F, Honig B, Shapiro L, Palmer AG 3rd. Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion. Proc. Natl. Acad. Sci. USA (2013) 110:16462-7. 

2012

Jin X, Walker MA, Felsövályi K, Vendome J, Bahna F, Mannepalli S, Cosmanescu F, Ahlsen G, Honig B, Shapiro L. Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca²+-free interdomain linkers. Proc. Natl. Acad. Sci. USA (2012) 109:E127-34. 

Brasch J, Harrison OJ, Honig B, Shapiro L. Thinking outside the cell: how cadherins drive adhesion. Trends Cell Biol. (2012) 22:299-310. 

Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 490:556-60.

Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L. Nectin ectodomain structures reveal a canonical adhesive interface. Nat. Struct. Mol. Biol. (2012) 19:906-15. 

Floratos A, Honig B, Pe'er D, Califano A. Using systems and structure biology tools to dissect cellular phenotypes. J. Am. Med. Inform. Assoc. (2012) 19:171-5. 

Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. 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 (2012) 13:1-7. 

Chen Y, Sheng R, Källberg M, Silkov A, Tun MP, Bhardwaj N, Kurilova S, Hall RA, Honig B, Lu H, Cho W. Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions. Mol. Cell (2012) 46:226-37. 

2011

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell (2011) 147:1270-82. 

Commentary

Ansari AZ, Peterson-Kaufman KJ. A partner evokes latent differences between Hox proteins. Cell (2011) 147:1220-1.

Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem. Biol. (2011) 6:1314-20. 

Kuziemko A, Honig B, Petrey D. Using structure to explore the sequence alignment space of remote homologs. PLoS Comput. Biol. (2011) 7:e1002175. 

Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. (2011) 39(Web Server issue):W283-7. 

Wu Y, Vendome J, Shapiro L, Ben-Shaul A, Honig B. Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature (2011) 475:510-3. 

Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat. Struct. Mol. Biol. (2011) 18:693-700. 

Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D. MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res. (2011) 39(Web Server issue):W357-61.

Honig B, Rohs R. Biophysics: Flipping Watson and Crick. Nature (2011) 470:472-3. 

Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, Honig B. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure (2011) 19:244-56. 

Brasch J, Harrison OJ, Ahlsen G, Carnally SM, Henderson RM, Honig B, Shapiro L. Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. J. Mol. Biol. (2011) 408:57-73. 

Behnke-Parks WM, Vendome J, Honig B, Maliga Z, Moores C, Rosenfeld SS. Loop L5 acts as a conformational latch in the mitotic kinesin Eg5. J. Biol. Chem. (2011) 286:5242-53. 

Zhu J, Yu Y, Ulbrich MH, Li MH, Isacoff EY, Honig B, Yang J. Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach. Proc. Natl. Acad. Sci. USA (2011) 108:10133-8. 

2010

Wu Y, Jin X, Harrison O, Shapiro L, Honig BH, Ben-Shaul A. Cooperativity between trans and cis interactions in cadherin-mediated junction formation. Proc. Natl. Acad. Sci. USA 2010 107:17592-7.

Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X. Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron (2010) 67:61-74. 

Commentary

Wei Z, Zhang M. A structural approach to decipher the neurexin and neuroligin splice isoform code. Neuron (2010) 67:1-2.

Norel R, Petrey D, Honig B. PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Res. (2010) 38(Web Server issue):W550-4.

Chen BY, Honig B. VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PLoS Comput. Biol. (2010) 6:e1000881.  

Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proc. Natl. Acad. Sci. USA (2010) 107:10896-901. 

Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D. High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J. Struct. Funct. Genomics (2010) 11:51-9.

Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat. Struct. Mol. Biol. (2010) 17:423-9. 

Commentary

Chitayata S, Arrowsmith CH. Four p(53)s in a pod. Nat. Struc. Mol. Biol. (2010)17:390-1.

Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Ann. Rev. Biochem. (2010) 79:233-69.

Harrison OJ, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll KJ, Price SR, Honig B, Shapiro L. Two-step adhesive binding by classical cadherins. Nat. Struct. Mol. Biol. (2010) 17:348-57. 

Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison OJ, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, Jessell TM, Honig B, Shapiro L. T-cadherin structures reveal a novel adhesive binding mechanism. Nat. Struct. Mol. Biol. (2010) 17:339-47. 

Zhu J, Cheng L, Fang Q, Zhou ZH, Honig B. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J. Mol. Biol. (2010) 397:835-51. 

West SM, Rohs R, Mann RS, Honig B. Electrostatic interactions between arginines and the minor groove in the nucleosome. J. Biomol. Struct. & Dyn. (2010) 27:861-6.

Cheng L, Zhu J, Hui WH, Zhang X, Honig B, Fang Q, Zhou ZH. Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. J. Mol. Biol. (2010) 397:852-63.

Singarapu KK, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione GT, Szyperski T. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. Proteins: Struc. Func. Bioinform. (2010) 78:779-84. 

Love J, Mancia F, Shapiro L, Punta M, Rost B, Girvin M, Wang DN, Zhou M, Hunt JF, Szyperski T, Gouaux E, MacKinnon R, McDermott A, Honig B, Inouye M, Montelione G, Hendrickson WA. The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J. Struct. Funct. Genomics (2010) 11:191-9. 

2009

Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature (2009) 461:1248-53. 

Commentaries

Tullius T. Structural Biology: DNA binding shapes up. Nature (2009) 461:1225-6.

Studies begin to shape new image of DNA. HHMI Research News (2009) October.

Yarnell AT. DNA shape directs proteins. Chem. Engin. News (2009) 87:26.

Petrey D, Fischer M, Honig B. Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc. Natl. Acad. Sci. USA (2009) 106:17377-82. 

Katsamba P, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price S, Jessell TM, Ben-Shaul A, Shapiro L, Honig BH. Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proc. Natl. Acad. Sci. USA (2009) 106:11594-9. 

Rohs R, West SM, Liu P, Honig B. Nuance in the double-helix and its role in protein-DNA recognition. Curr. Opin. Struct. Biol. (2009) 19:171-7.

Petrey D, Honig B. Is protein classification necessary? Toward alternative approaches to function annotation. Curr. Opin. Struct. Biol. (2009) 19:363-8.  

Rossi P, Aramini JM, Xiao R, Chen CX, Nwosu C, Owens LA, Maglaqui M, Nair R, Fischer M, Acton TB, Honig B, Rost B, Montelione GT. Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins: Struc. Func. Bioinform. (2009) 74:515-9.

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 17:151-9.

2008

Kosloff M, Alexov E, Arshavsky VY, Honig B. Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. J. Biol. Chem. (2008) 283:31197-207. 

Miloushev VZ, Bahna F, Ciatto C, Ahlsen G, Honig B, Shapiro L, Palmer AG 3rd. Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure (2008) 16:1195-205. 

Forrest LR, Zhang YW, Jacobs MT, Gesmonde J, Xie L, Honig BH, Rudnick G. Mechanism for alternating access in neurotransmitter transporters. Proc. Natl. Acad. Sci. USA (2008) 105:10338-43. 

Commentaries

Kanner BI. Structural biology: it's not all in the family. Nature (2008) 454:593-4.

Research Highlights. Nat. Struct. Mol Biol. (2008) 15:785.

Posy S, Shapiro L, Honig B. Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? J. Mol. Biol. (2008) 378:954-68. 

Zhu J, Fan H, Periole X, Honig B, Mark AE. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins: Struc. Func. Bioinform. (2008) 72:1171-88. 

Koehnke J, Jin X, Trbovic N, Katsamba PS, Brasch J, Ahlsen G, Scheiffele P, Honig B, Palmer AG 3rd, Shapiro L. Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4. Structure (2008) 16:410-21. 

Koehnke J, Jin X, Budreck EC, Posy S, Scheiffele P, Honig B, Shapiro L. Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Proc. Natl. Acad. Sci. USA (2008) 105:1873-8. 

Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B. Loop modeling: Sampling, filtering, and scoring. Proteins: Struc. Func. Bioinform. (2008) 70:834-43.

2007

Shapiro L, Honig B. Cell-to-Cell Contact and Extracellular Matrix. Curr. Opin. Cell Biol. (2007) 19:493-94.

Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell (2007) 131:530-43.

Commentary

In This Issue. Cell (2007) 131:421-3.

Forrest LR, Tavoulari S, Zhang YW, Rudnick G, Honig B. Identification of a chloride ion binding site in Na+/Cl -dependent transporters. Proc. Natl. Acad. Sci. USA (2007) 104:12761-6. 

Commentaries

Biochemistry Select. Cell (2007) 963:954-63.

Chin G, Yeston J. Editor's Choice. Science (2007) 317:872-3.

Amara SG. Chloride finds its place in the transport cycle. Nat. Struct. Mol. Biol. (2007) 14:792-4.

Honig B. Protein structure space is much more than the sum of its folds. Nat. Struct. Mol. Biol. (2007) 14:458. 

Fasnacht M, Zhu J, Honig B. Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci. (2007) 16:1557-68. 

Singarapu KK, Liu G, Xiao R, Bertonati C, Honig B, Montelione GT, Szyperski T. NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif. Proteins: Struc. Func. Bioinform. (2007) 67:501-4. 

Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins: Struc. Func. Bioinform.  (2007) 66:814-23.

Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc. Natl. Acad. Sci. USA (2007) 104:6305-10. 

Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys. J. (2007) 92:1891-9. 

Siggers TW, Honig B. Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res. (2007) 35:1085-97. 

Tang CL, Alexov E, Pyle AM, Honig B. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. J. Mol. Biol. (2007) 366:1475-96.

2006

Johnston RJ Jr, Copeland JW, Fasnacht M, Etchberger JF, Liu J, Honig B, Hobert O. An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Development (2006) 133:3317-28. 

Lin YC, Liu G, Shen Y, Bertonati C, Yee A, Honig B, Arrowsmith CH, Szyperski T; Northeast Structural Genomics Consortium. NMR structure of protein PA2021 from Pseudomonas aeruginosa. Proteins: Struc. Func. and Genet. (2006) 65:767-70. 

Kolodny R, Honig B. VISTAL--a new 2D visualization tool of protein 3D structural alignments. Bioinformatics (2006) 22:2166-7. 

Kolodny R, Petrey D, Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr. Opin. Struct. Biol. (2006) 16:393-8.

Forrest LR, Tang CL, Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys. J. (2006) 91:508-17. 

Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins: Struc. Func. Bioinform. (2006) 65:463-79.

Ortiz CO, Etchberger JF, Posy SL, Frøkjaer-Jensen C, Lockery S, Honig B, Hobert O. Searching for neuronal left/right asymmetry: genomewide analysis of nematode receptor-type guanylyl cyclases. Genetics (2006) 173:131-49. 

Patel SD, Ciatto C, Chen CP, Bahna F, Rajebhosale M, Arkus N, Schieren I, Jessell TM, Honig B, Price SR, Shapiro L. Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell (2006) 124:1255-68.

Nayal M, Honig B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins: Struc. Func. Bioinform. (2006) 63:892-906.

2005

Powers R, Mirkovic N, Goldsmith-Fischman S, Acton TB, Chiang Y, Huang YJ, Ma L, Rajan PK, Cort JR, Kennedy MA, Liu J, Rost B, Honig B, Murray D, Montelione GT. Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes. Protein Sci. (2005) 14:2849-61.

Murray PS, Li Z, Wang J, Tang CL, Honig B, Murray D. Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle. Structure (2005) 13:1521-31.

Petrey D, Honig B. Protein structure prediction: inroads to biology. Mol Cell. (2005)  20:811-9. 

Siggers T, Silkov T, Honig B. Bending in the right direction. Structure (2005) 13:1400-1.

Chen CP, Posy S, Ben-Shaul A, Shapiro L, Honig BH. Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping. Proc. Natl. Acad. Sci. USA (2005) 102:8531-6.

Forrest LR, Honig B. An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins: Struc. Func. Bioinform. (2005) 61:296-309.

Wildonger J, Sosinsky A, Honig B, Mann RS. Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes Dev. (2005) 19:1034-9.

Shen Y, Goldsmith-Fischman S, Atreya HS, Acton T, Ma L, Xiao R, Honig B, Montelione GT, Szyperski T. 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. Bioinform. (2005) 58:747-50. 

Murray D, Honig B. To B or not to B: PIP2 answers the question. Dev. Cell (2005) 8:138-9.

Zhu J, Alexov E, Honig B. Comparative study of generalized born models: Born radii and peptide folding. J. Phys. Chem. B. (2005) 109:3008-22.

Fan H, Mark AE, Zhu J, Honig B. Comparative study of generalized Born models: protein dynamics. Proc. Natl. Acad. Sci. USA (2005) 102:6760-4.

Siggers TW, Silkov A, Honig B. Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity. J. Mol. Biol. (2005) 345:1027-45. 

2004

Gimpelev M, Forrest LR, Murray D, Honig B. Helical packing patterns in membrane and soluble proteins. Biophys. J. (2004) 87:4075-86. 

Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N. An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys. J. (2004) 87:3448-59. 

Ramelot TA, Cort JR, Goldsmith-Fischman S, Kornhaber GJ, Xiao R, Shastry R, Acton TB, Honig B, Montelione GT, Kennedy MA. Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. J. Mol. Biol. (2004)  344:567-83.

Goldsmith-Fischman S, Kuzin A, Edstrom WC, Benach J, Shastry R, Xiao R, Acton TB, Honig B, Montelione GT, Hunt JF. The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes. J. Mol. Biol. (2004) 344:549-65.

Liu G, Sukumaran DK, Xu D, Chiang Y, Acton T, Goldsmith-Fischman S, Honig B, Montelione GT, Szyperski T. NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins (2004) 55:756-8. 

Xu D, Liu G, Xiao R, Acton T, Goldsmith-Fischman S, Honig B, Montelione GT, Szyperski T. 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. 2004) 54:794-6. 

Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins: Struc. Func. Bioinform. (2004) 55:351-67.

2003

Aramini JM, Huang YJ, Cort JR, Goldsmith-Fischman S, Xiao R, Shih LY, Ho CK, Liu J, Rost B, Honig B, Kennedy MA, Acton TB, Montelione GT. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci. (2003) 12:2823-30.

Patel SD, Chen CP, Bahna F, Honig B, Shapiro L. Cadherin-mediated cell-cell adhesion: sticking together as a family. Curr. Opin. Struct. Biol. (2003) 13:690-8. 

Tang CL, Xie L, Koh IY, Posy S, Alexov E, Honig B. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J. Mol. Biol. (2003) 334:1043-62.

Sheinerman FB, Al-Lazikani B, Honig B. Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. J. Mol. Biol. (2003) 334:823-41.

Petrey D, Honig B. GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol. (2003) 374:492-509.

Ramelot TA, Ni S, Goldsmith-Fischman S, Cort JR, Honig B, Kennedy MA. Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold. Protein Sci. (2003) 12:1556-61.

Tao X, Khayat R, Christendat D, Savchenko A, Xu X, Goldsmith-Fischman S, Honig B, Edwards A, Arrowsmith CH, Tong L. Crystal structures of MTH1187 and its yeast ortholog YBL001c. Proteins: Struc., Func. and Genet. (2003) 52:478-80. 

Goldsmith-Fischman S, Honig B. Structural genomics: computational methods for structure analysis. Protein Sci. (2003) 12:1813-21. 

Sosinsky A, Bonin CP, Mann RS, Honig B. Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res. (2003) 31:3589-92.

Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins: Struc., Func. and Genet. (2003) 53:430-5.

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

2002

Rost B, Honig B, Valencia A. Bioinformatics in structural genomics. Bioinformatics (2002) 18:897-8. 

Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J. Mol. Biol. (2002) 320:597-608.

Murray D, Arbuzova A, Honig B, McLaughlin S. The role of electrostatic and nonpolar interactions in the association of peripheral proteins with membranes. Curr. Topics Membranes (2002) 52:277-307.

Xiang Z, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc. Natl. Acad. Sci. USA (2002) 99:7432-7.

Sheinerman FB, Honig B. On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mol. Biol. (2002) 318:161-77.

Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. 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. Comput. Chem. (2002) 23:128-37.

Murray D, Honig B. Electrostatic control of the membrane targeting of C2 domains. Mol. Cell  (2002) 9:145-54.

2001

Al-Lazikani B, Sheinerman FB, Honig B. 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 (2001) 98:14796-801.

Murray D, McLaughlin S, Honig B. The role of electrostatic interactions in the regulation of the membrane association of G protein beta gamma heterodimers. J. Biol. Chem. (2001) 276:45153-9. 

Rocchia W, Alexov E, Honig B. Extending the Applicability of the Nonlinear Poisson-Boltzman Equation: Multiple Dielectric Constants and Multivalent Ions. J. Phys. Chem. B. (2001) 105:6507-14.

Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J. Mol. Biol. (2001) 311:421-30. 

Norel R, Sheinerman F, Petrey D, Honig B. Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis. Protein Sci. (2001) 10:2147-61.

Gerstein M, Honig B. Sequences and Topology. Curr. Opinion Struc. Biol. (2001) 11:327-29.

Al-Lazikani B, Jung J, Xiang Z, Honig B. Protein structure prediction. Curr. Opin. Chem. Biol. (2001) 5:51-6. 

2000

Petrey D, Honig B. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci. (2000) 9:2181-91.

Ben-Tal N, Honig B, Bagdassarian CK, Ben-Shaul A. Association entropy in adsorption processes. Biophys. J. (2000) 79:1180-7.

Arbuzova A, Wang L, Wang J, Hangyás-Mihályné G, Murray D, Honig B, McLaughlin S. 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 (2000) 39:10330-9.

Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol. (2000) 30:691-711.

Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol. (2000) 301:679-89.

Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J. Mol. Biol. (2000) 301:665-78.

Sheinerman FB, Norel R, Honig B. Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol. (2000) 10:153-9. 

1999

Murray D, Arbuzova A, Hangyás-Mihályné G, Gambhir A, Ben-Tal N, Honig B, McLaughlin S. Electrostatic properties of membranes containing acidic lipids and adsorbed basic peptides: theory and experiment. Biophys. J. 1999 77:3176-88.

Polticelli F, Ascenzi P, Bolognesi M, Honig B. Structural determinants of trypsin affinity and specificity for cationic inhibitors. Protein Sci. (1999) 8:2621-9.

Chin K, Sharp KA, Honig B, Pyle AM. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nat. Struct. Biol. (1999) 6:1055-61.

Honig B. Protein folding: from the levinthal paradox to structure prediction. J. Mol. Biol. (1999) 293:283-93. 

Yang AS, Honig B. Sequence to structure alignment in comparative modeling using PrISM. Proteins: Struc. Func. and Genet. (1999) Suppl 3:66-72.

Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Improving macromolecular electrostatics calculations. Protein Eng. (1999) 12:657-62.

Xiao L, Honig B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. (1999) 289:1435-44.

Nayal M, Hitz BC, Honig B. GRASS: a server for the graphical representation and analysis of structures. Protein Sci. (1999) 8:676-9.

1998

Misra VK, Hecht JL, Yang AS, Honig B. Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA. Biophys. J. (1998) 75:2262-73.

Murray D, Hermida-Matsumoto L, Buser CA, Tsang J, Sigal CT, Ben-Tal N, Honig B, Resh MD, McLaughlin S. Electrostatics and the membrane association of Src: theory and experiment. Biochemistry (1998) 37:2145-59.

1997

Honig B. New challenges in computational biochemistry. Pac. Symp. Biocomput. (1997) 1997:21-4. 

Murray D, Ben-Tal N, Honig B, McLaughlin S. Electrostatic interaction of myristoylated proteins with membranes: simple physics, complicated biology. Structure (1997) 5:985-9. Review.

Chen S-w W, Honig B. Monovalent and Divalent Salt Effects on Electrostatic Free Energies Defined by the Nonlinear Poisson-Boltzmann Equation: Application to DNA Reactions. J Phys. Chem. B. (1997) 101:9113-8.

Ben-Tal N, Honig B, Miller C, McLaughlin S. Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles. Biophys. J. (1997) 73:1717-27.

Froloff N, Windemuth A, Honig B. On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions. Protein Sci. (1997) 6:1293-301.

Ben-Tal N, Sitkoff D, Topol IA, Yang AS, Burt SK, Honig B. Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution. J. Phys. Chem. B. (1997) 101:450-7.

1996

Ben-Tal N, Honig B. Helix-helix interactions in lipid bilayers. Biophys. J. (1996) 71:3046-50.

Friedman RA, Honig B. Response to S.H. Gellman, T.S. Haque, and L.F. Newcomb. Biophys. J. (1996) 71:3525-6.

Ben-Tal N, Honig B, Peitzsch RM, Denisov G, McLaughlin S. Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results. Biophys. J. (1996) 71:561-75.

Sharp KA, Kumar S, Rossky PJ, Friedman RA, Honig B. Size Dependence of Transfer Free Energies. 2 Hard Sphere Models. J. Phys. Chem. (1996) 100:14166-77.

Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. 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. (1996) 100:11775-88.

Honig B, Cohen FE. Adding backbone to protein folding: why proteins are polypeptides. Fold. Des. (1996) 1:R17-20.

Lancaster CR, Michel H, Honig B, Gunner MR. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis. Biophys. J. (1996) 70:2469-92.

Gunner MR, Nicholls A, Honig B. Electrostatic Potentials in Rhodopseudomonas viridis Reaction Centers: Implications for the Driving Force and Directionality of Electron Transfer. J. Phys. Chem. (1996) 100:4277-91.

Sampogna RV, Honig B. Electrostatic coupling between retinal isomerization and the ionization state of Glu-204: a general mechanism for proton release in bacteriorhodopsin. Biophys. J. (1996) 71:1165-71.

Yang AS, Hitz B, Honig B. Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding. J. Mol. Biol. (1996) 259:873-82.

Ben-Shaul A, Ben-Tal N, Honig B. Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes. Biophys. J. (1996) 71:130-7.

Ben-Tal N, Ben-Shaul A, Nicholls A, Honig B. Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophys. J. (1996) 70:1803-12.

Misra VK, Honig B. The electrostatic contribution to the B to Z transition of DNA. Biochemistry (1996) 35:1115-24.

Sitkoff D, Ben-Tal N, Honig B. Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models. J. Phys. Chem. (1996) 100:2744-52.

1995

Honig B, Ottolenghi M, Sheves M. Acid-Base Equilibria and the Proton Pump in Bacteriorhodopsin. Israel J. Chem. (1995) 35:429-46.

Yang AS, Honig B. Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets. J. Mol. Biol. (1995) 252:366-76.

Yang AS, Honig B. Free energy determinants of secondary structure formation: I. alpha-Helices. J. Mol. Biol. (1995) 252:351-65.

Sharp KA, Honig B. Salt effects on nucleic acids. Curr. Opin. Struct. Biol. (1995) 5:323-8. Review.

Friedman RA, Honig B. A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys. J. (1995) 69:1528-35.

Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science (1995) 268:1144-9.

Vorobjev YN, Scheraga HA, Honig B. Theoretical Modeling of the Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in Polar Ionic Solution. pH-Induced Helix-Coil Transition of Poly (l-lysine) in Water and Methanol Ionic Solutions. J. Phys. Chem. (1995) 99:7180-87.

Sharp KA, Friedman RA, Misra V, Hecht J, Honig B. Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann, and limiting law/counterion binding models. Biopolymers (1995) 36:245-62.

Hecht JL, Honig B, Shin YK, Hubbell WL. Electrostatic Potentials Near the Surface of DNA: Comparing Theory and Experiment. J. Phys. Chem. (1995) 99:7782-86.

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

Honig B, Yang AS. Free energy balance in protein folding. Adv. Protein. Chem. (1995) 46:27-58. 

Kumar SK, Szleiffer I, Sharp KA, Rossky P, Friedman R, Honig B. Size Dependence of Transfer Free Energies A Flory-Huggins Approach. J. Phys. Chem. (1995) 99:8382-91.

Misra VK, Honig B. On the magnitude of the electrostatic contribution to ligand-DNA interactions. Proc. Natl. Acad. Sci. USA (1995) 92:4691-5.

1994

Vorobjev YN, Scheraga HA, Hitz B, Honig B. 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. (1994) 98:10940-8.

Rajasekaran E, Jayaram B, Honig B. Electrostatic Interactions in Aliphatic Dicarboxylic Acids: A Computational Route to the determination of pKa shifts. J. Am. Chem. Soc. (1994) 116:8238-40.

Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Ringnalda M, Goddard III WA, Honig B. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectic Theory. J. Am. Chem. Soc. (1994) 116:11875-82.

Sampogna RV, Honig B. Environmental effects on the protonation states of active site residues in bacteriorhodopsin. Biophys. J. (1994) 66:1341-52.

Sitkoff D, Sharp KA, Honig B. Correlating solvation free energies and surface tensions of hydrocarbon solutes. Biophys. Chem. (1994) 51:397-403; discussion 404-9.

Sitkoff D, Lockhart DJ, Sharp KA, Honig B. Calculation of electrostatic effects at the amino terminus of an alpha helix. Biophys. J. (1994) 67:2251-60.

Scott DL, Mandel AM, Sigler PB, Honig B. The electrostatic basis for the interfacial binding of secretory phospholipases A2. Biophys. J. (1994) 67:493-504.

Yang AS, Honig B. Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin. J. Mol. Biol. (1994) 237:602-14.

Sitkoff D, Sharp KA, Honig B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. (1994) 98:1978-88.

Misra VK, Hecht JL, Sharp KA, Friedman RA, Honig B. Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease. J. Mol. Biol. (1994)  238:264-80.

Misra VK, Sharp KA, Friedman RA, Honig B. Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J. Mol. Biol. (1994) 238:245-63.

Monge A, Friesner RA, Honig B. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc. Natl. Acad. Sci. USA (1994)  91:5027-9.

Smith KS, Honig B. Evaluation of the conformational free energies of loops in proteins. Proteins: Struc., Func. and Genet. (1994) 18:119-32.

1993

Gilliam TC, Tanzi RE, Petrukhin K, Chernov I, Pellequer JL, Wasco W, Ross B, Romano DM, Parano E, Brzustowicz LM, Devoto M, Peppercorn J, Bush AI, Sternieb I, Pirastu M, Gusella JF, Evgrafov O, Penchaszadeh GK, Honig B, Edelman IS, Soares MB, Scheinberg IH. The Wilson Disease Gene is a Copper Transporting ATPase with Homology to the Menkes' Disease Gene. Nat. Genet. (1993) 5:344-350.

Honig B, Sharp KA, Yang A-S. Macroscopic Models of Aqueous Solutions: Biological and Chemical Applications. J. Phys. Chem. (1993) 97:1101-9.

Yang AS, Honig B. On the pH dependence of protein stability. J. Mol. Biol. (1993) 231:459-74.

Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B. On the calculation of pKas in proteins. Proteins: Struc., Func. and Genet. (1993) 15:252-65.

Gunner M, Honig B. Calculations of Proton Uptake in Rhodobacter Sphaeroides Reaction Centers. In The Photosynthetic Bacterial Reaction Centre: Structure, Spectroscopy, and Dynamic. Breton J and Vermeglio, editors. Plenum Publishing Company Ltd., England (1993) p.403-10.

1992

Yang AS, Sharp KA, Honig B. Analysis of the heat capacity dependence of protein folding. J. Mol. Biol. (1992) 227:889-900. 

Yang AS, Honig B. Electrostatic effects on protein stability. Curr. Opin. Struc. Biol. (1992) 2:40-5.

Sharp K, Jean-Charles A, Honig B. A Local Dielectric Constant Model for Solvation Free Energies Which Accounts for Solute Polarizability. J. Phys. Chem. (1992) 96:3822-8.

McGrath ME, Vásquez JR, Craik CS, Yang AS, Honig B, Fletterick RJ. Perturbing the polar environment of Asp102 in trypsin: consequences of replacing conserved Ser214. Biochemistry (1992) 31:3059-64.

Friedman RA, Honig B. The electrostatic contribution to DNA base-stacking interactions. Biopolymers (1992) 32:145-59.

1991

Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struc., Func. and Genet. (1991) 11:281-96.

Sharp KA, Nicholls A, Friedman R, Honig B. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry (1991) 30:9686-97. 

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

Sharp KA, Nicholls A, Fine RF, Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science (1991) 252:106-9.

Nicholls A, Honig B. A Rapid Finite Difference Alogrithm, Utililizing Successive Over-Relaxation to Solve the Poisson-Boltzman Equation. J. Comp. Chem. (1991) 12:435-45.

Jean-Charles A, Nicholls A, Sharp K, Honig B, Tempczyk A, Hendrickson TF, Still WC. Electrostatic Contributions to Solvation Energies: Comparison of Free Energy Perturbation and Continuum Calculations. J. Am. Chem. Soc. (1991) 113:1454-5.

Honig B. In Memoriam: Cyrus Levinthal. Proteins: Struc Func Genet. (1991) 11:239-41.

Gunner MR, Honig B. Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center. Proc. Natl. Acad. Sci. USA (1991) 88:9151-5.

Gilson MK, Honig B. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Comput. Aided Mol. Des. (1991) 5:5-20.

1990

Sharp K, Honig B. Applications of the Finite Defference Poisson-Boltzman Method to Proteins and Nucleic Acids. In Structure and Methods Vol 2: DNA Protein Complexes & Proteins. Sarma RH and Sarma MH, editors. Adenine Press. (1990) p.211-214.

Sharp KA, Honig B. Calculating Total Electrostatic Energies with the Nonlinear Poisson-Boltzmann Equation. J. Phys. Chem. (1990) 94:7684-92.

Sharp KA, Honig B. Electrostatic interactions in macromolecules: theory and applications. Ann. Rev. Biophys. Biophys. Chem. (1990) 19:301-32. 

Koutalos Y, Ebrey TG, Gilson HR, Honig B. Octopus photoreceptor membranes. Surface charge density and pK of the Schiff base of the pigments. Biophys. J. (1990) 58:493-501.

Jayaram B, Swaminathan S, Beveridge D, Sharp K, Honig B. Monte Carlo simulation studies on the structure of the counterion of B-DNA. Variations on the primitive dielectric model. Macromolecules (1990) 23: 3156-65.

Honig B. Environmental Effects on Electrostatic Interactions. In Theoretical Biochemistry & Molecular Biophysics Volume 2: Proteins. Beveridge DL and Lavery R, editors. Adenine Press (1990) p.63-67.

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

Sharp KA, Honig B, Harvey SC. Electrical potential of transfer RNAs: codon-anticodon recognition. Biochemistry (1990) 29:340-6.

1989

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

Soman K, Yang AS, Honig B, Fletterick R. Electrical potentials in trypsin isozymes. Biochemistry (1989) 28:9918-26.

Chen JG, Nakamura T, Ebrey TG, Ok H, Konno K, Derguini F, Nakanishi K, Honig B. Wavelength regulation in iodopsin, a cone pigment. Biophys. J. (1989) 55:725-9.

Koutalos Y, Ebrey TG, Tsuda M, Odashima K, Lien T, Park MH, Shimizu N, Derguini F, Nakanishi K, Gilson H, Honig B. Regeneration of Bovine and Octopus Opsins in Situ with Natural and Artificial Retinals. Biochem. (1989) 28:2732-39.

Gilson MK, Honig B. Destabilization of an alpha-helix-bundle protein by helix dipoles. Proc. Natl. Acad. Sci. USA (1989) 86:1524-8.

Honig B, Sharp K, Gilson M. Electrostatic interactions in proteins. In 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 (1989) p.65-74.

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

Jayaram B, Fine R, Sharp KA, Honig B. Free Energy Calculations of Ion Hydration: An Analysis of the Born Model in Terms of Microscopic Simulations. J. Phys. Chem. (1989) 93:4320-7.

1988

Lanyi JK, Zimányi L, Nakanishi K, Derguini F, Okabe M, Honig B. Chromophore/protein and chromophore/anion interactions in halorhodopsin. Biophys. J. (1988) 53:185-91.

Gilson H, Honig BH. Analysis of NMR and Absorption Spectroscopic Data in Bacteriorhodopsin: Models for Protein Chromophore Interactions. J. Am. Chem. Soc. (1988) 110:1943-50.

Eccles J, Honig B, Schulten K. Spectroscopic determinants in the reaction center of rhodopseudomonas viridis. Biophys. J. (1988) 53:137-44.

Gilson HS, Honig BH, Croteau A, Zarrilli G, Nakanishi K. Analysis of the factors that influence the C=N stretching frequency of polyene Schiff bases. Implications for bacteriorhodopsin and rhodopsin. Biophys. J. (1988) 53:261-9.

Gilson MK, Honig BH. Energetics of charge-charge interactions in proteins. Proteins: Struc., Func. and Genet. (1988) 3:32-52. 

Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins: Struc., Func. and Genet. (1988) 4:7-18.

1987

Gilson M, Sharp KA, Honig B. Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment. J. Comp. Chem. (1987) 9:327-35.

Sharp K, Gilson M, Fine R, Honig, B. Electrostatic Interactions in Proteins. In Protein Structure, Folding and Design 2, (UCLA Symposia on Mol. Cell. Biol.) Alan R. Liss, Inc. (1987) 2:235-44.

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

Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature (1987) 330:84-6.

Sharp K, Fine R, Honig B. Computer simulations of the diffusion of a substrate to an active site of an enzyme. Science (1987) 236:1460-3.

Sharp K, Fine R, Schulten K, Honig B. Brownian Dynamics Simulations of Diffusion to Irregular Bodies. J. Phys. Chem. (1987) 91:3624-31.

1986

Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. 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. (1986) 1:47-59.

Spudich JL, McCain DA, Nakanishi K, Okabe M, Shimizu N, Rodman H, Honig B, Bogomolni RA. Chromophore/protein interaction in bacterial sensory rhodopsin and bacteriorhodopsin. Biophys. J. (1986)49:479-83.

Gilson M, Honig B. The Dielectric Constant of a Folded Protein. Biopolymers (1986) 25:2097-110.

Honig BH, Hubbell WL, Flewelling RF. Electrostatic interactions in membranes and proteins. Ann. Rev. Biophys. Biophys. Chem. (1986) 15:163-93. Review. 

Rashin AA, Iofin M, Honig B. Internal Cavities and Buried Waters in Globular Proteins. Biochem. (1986) 25:3619-23.

1985

Schiffmiller R, Callender RH, Waddell WH, Govindjee R, Ebrey TG, Kakitani H, Honig B, Nakanishi K. Resonance Raman studies of bacteriorhodopsin analogues. Photochem. Photobiol. (1985) 41:563-7. 

Gilson MK, Rashin A, Fine R, Honig B. On the calculation of electrostatic interactions in proteins. J. Mol. Biol. (1985) 184:503-16.

Rashin AA, Honig B. Reevaluation of the Born Model of Ion Hydration. J. Phys. Chem. (1985) 89:5588-93.

Kakitani H, Kakitani T, Rodman H, Honig B. On the mechanism of wavelength regulation in visual pigments.  Photochem. Photobiol. (1985) 41:471-9.

1984

Doukas AG, Junnarkar MR, Alfano RR, Callender RH, Kakitani T, Honig B. Fluorescence quantum yield of visual pigments: evidence for subpicosecond isomerization rates. Proc. Natl. Acad. Sci. USA (1984) 81:4790-4.

Honig BH, Hubbell WL. Stability of "salt bridges" in membrane proteins. Proc. Natl. Acad. Sci. (1984) 81:5412-6.

Rashin AA, Honig B. On the environment of ionizable groups in globular proteins. J. Mol. Biol. (1984) 173:515-21.

Honig B. Electrostatic interactions in membrane proteins. Prog. Clin. Biol. Res. (1984) 164:149-52. 

1983

Kakitani H, Kakitani T, Rodman H, Honig B, Callender R. Correlation of Vibrational Frequencies with Absorption Maxima in Polyenes, Rhodopsin, Bacteriorhodopsin and Retinal Analogues. J. Phys. Chem. (1983) 87:3620-8.

Kakitani T, Kakitani H, Honig B, Nakanishi K. Symmetric Charge Distribution in Bacteriorhodopsin Binding Site. J. Am. Chem. Soc. (1983) 105:648-50.

Eccles J, Honig B. Charged amino acids as spectroscopic determinants for chlorophyll in vivo. Proc. Natl. Acad. Sci. USA (1983) 80:4959-62.

1982

Kakitani T, Honig B, Crofts AR. Theoretical studies of the electrochromic response of carotenoids in photosynthetic membranes. Biophys. J. (1982) 39:57-63.

Honig B. Theoretical Aspects of Photoisomerization in Visual Pigments and Bacteriorhodopsin. In Biological Aspects of Ultrafast Laser Spectroscopy. Alfano R, Editor. Academic Press, New York. (1982) p.281.

Honig B. Photochemical Charge Separation and Active Transport in the Purple Membrane. In Current Topics in Membranes and Transport. Academic Press, Inc. (1982) 16:371-386.

1981

Balogh-Nair V, Carriker JD, Honig B, Ramat V, Motto MG, Nakanishi K, Sen R, Sheves M, Tanis MA, Tsujimoto K. The 'Opsin Shift' in Bacteriorhodopsin: Studies with Artificial Bacteriorhodopsins. Photochem. Photobiol. (1981) 33:483-8.

Doukas AG, Pande A, Suzuki T, Callender RH, Honig B, Ottolenghi M. On the mechanism of hydrogen-deuterium exchange in bacteriorhodopsin. Biophys. J. (1981) 33:275-9.

Kalisky O, Ottolenghi M, Honig B, Korenstein R. Environmental effects on formation and photoreaction of the M412 photoproduct of bacteriorhodopsin: implications for the mechanism of proton pumping. Biochemistry (1981) 20:649-55.

Honig B. Excited state properties of visual pigments and bacteriorhodopsin. Ann. NY Acad. Sci. (1981) 367:269-80. 

Dinur U, Honig B, Ottolenghi M. Analysis of Primary Photochemical Processes in Bacteriorhodopsin. Photochem. Photobiol. (1981) 33:523-7.

1980

Honig B, Dinur U, Birge R, Ebrey TG. The Isomer Dependence of Oscillator Strengths in Retinal and Related Molecules. Spectroscopic Assignments. J. Am. Chem. Soc. (1980) 102:488-94.

Nakanishi K, Balogh-Nair V, Arnaboldi M, Tsujimoto K, Honig B. An external point charge model for bacteriorhodopsin to account for its purple color. J. Am. Chem. Soc. (1980) 102:7945-47.

Schulten K, Dinur U, Honig B. The Spectra of Carbonium Ions, Cyanine Dyes, and Protonated Schiff Base Polyenes. J. Chem. Phys. (1980) 73:3927-35.

Dinur U, Honig B, Schulten K. On the Nature of Excited Electronic States in Cyanine Dyes: Implications for Visual Pigment Spectra. Chem. Phys. Lett. (1980) 72:493-7.

Dinur U, Honig B. A Consistent Semiempirical Theory for the Calculation of Ground and Excited State Properties. J. Chem. Phys. (1980) 72:1817-29.

Aton B, Doukas AG, Narva D, Callender RH, Dinur U, Honig B. Resonance Raman studies of the primary photochemical event in visual pigments. Biophys. J. (1980) 29:79-94.

1979

Sheves M, Nakanishi K, Honig B. Through Space Electrostatic Effects in Electronic Spectra. Experimental Evidence for the External Point Charge Model of Visual Pigments. J.  Am. Chem. Soc. (1979) 101:7086-88.

Honig B, Dinur U, Nakanishi K, Balogh-Nair V, Gawinowicz MA, Arnaboldi M, Motto M. An External Point-Charge Model for Wavelength Regulation in Visual Pigments. J. Am. Chem. Soc. (1979) 101:7084-6.

Honig B, Ebrey T, Callender RH, Dinur U, Ottolenghi M. Photoisomerization, energy storage, and charge separation: a model for light energy transduction in visual pigments and bacteriorhodopsin. Proc. Natl. Acad. Sci. USA. (1979) 76:2503-7.

Dinur U, Honig B. Natural Orbitals of s-cis-Butadiene and Their Relation to Photochemical Cyclization. Chem. Phys. Lett. (1979) 64:588-92.

Dinur U, Honig B. On the Effects of Methyl Substitution on the Exited States of Butadiene. J. Am. Chem. Soc. (1979) 101:4453-60.

Nakanishi K, Balogh-Nair V, Gawinowicz MA, Arnaboldi M, Motto M, Honig B. Double point charge model for visual pigments; evidence from dihydrorhodopsins. Photochem. Photobiol. (1979) 29:657-60.

1978

Yonath A, Podjarny A, Honig B, Traub W, Sielecki A, Herzberg O, Moult J. Structural analysis of denaturant-protein interactions: comparison between the effects of bromoethanol and SDS on denaturation and renaturation of triclinic lysozyme. Biophys. Struct. Mech. (1978) 4:27-36.

Honig B. Kinetic and molecular models for proton pumping in Bacteriorhodopsin. In Energetics and structures of halophilic microorganisms. SR Kaplan and M Ginzburg, Editors. Elsevier/North-Holland Biomedical Press (1978) p.109-121.

Aton B, Callender RH, Honig B. Photochemical cis-trans isomerisation of bovine rhodopsin at liquid helium temperatures. Nature (1978) 273:784-6. 

Doukas AG, Aton B, Callender R, Honig, B. The Resonance Raman Excitation Profile of All-Trans Retinal: Theoretical Implications. Chem. Phys. Lett. (1978) 56:248-52.

Honig B, Stein WD. Design principles for active transport systems. J. Theor. Biol. (1978) 75:299-305. 

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

Hagler AT, Honig B. On the formation of protein tertiary structure on a computer. Proc. Natl. Acad. Sci. USA (1978) 75:554-8.

1977

Yonath A, Podjarny A, Honig B, Sielecki A, Traub W. Crystallographic studies of protein denaturation and renaturation. 2. Sodium dodecyl sulfate induced structural changes in triclinic lysozyme. Biochemistry (1977) 16:1418-24.

Hurley JB, Ebrey TG, Honig B, Ottolenghi M. Temperature and wavelength effects on the photochemistry of rhodopsin, isorhodopsin, bacteriorhodopsin and their photoproducts. Nature (1977) 270:540-2. 

Ebrey TG, Becher B, Mao B, Kilbride P, Honig B. Exciton interactions and chromophore orientation in the purple membrane. J. Mol. Biol. (1977) 112:377-97.

Stein WD, Honig B. Models for the active transport of cations...the steady-state analysis. Mol. Cell. Biochem. (1977) 15:27-44.

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

Rosenfeld T, Honig B, Ottolenghi M, Hurley J, Ebrey T. Cis-Trans Isomerization in the Photochemistry of Vision. Pure. and Appl. Chem. (1977) 49:341-51.

Hagler A, Honig B. Theoretical Studies of Protein Folding. In: Peptides Proc. of Fifth American Peptide Symposium. Goodman M and Meienhofer J, editors. Wiley, New York. 1977. p.280-3.

Ebrey TG, Honig B. New wavelength dependent visual pigment nomograms. Vision Res. (1977) 17:147-51. 

1976

Honig B, Greenberg AD, Dinur U, Ebrey TG. Visual-pigment spectra: implications of the protonation of the retinal Schiff base. Biochemistry (1976) 15:4593-9.

Honig B, Ray A, Levinthal C. Conformational flexibility and protein folding: rigid structural fragments connected by flexible joints in subtilisin BPN. Proc. Natl. Acad. Sci. USA (1976) 73:1974-8.

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

1975

Greenberg AD, Honig B, Ebrey TG. Wavelength dependence of the bandwidths of visual pigment spectra. Nature (1975) 257:823-4. 

Ebrey T, Govindjee R, Honig B, Pollock E, Chan W, Crouch R, Yudd A, Nakanishi K. Properties of Several Sterically Modified Retinal Analogs and their Photosensitive Pigments. Biochem. (1975) 14:3933-41.

Ebrey TG, Honig B. Molecular aspects of photoreceptor function. Quart. Rev. Biophys. (1975) 8:129-84. 

Alchalel A, Honig B, Ottolenghi M, Rosenfeld T. Triplet-sensitized cis-trans isomerization of the protonated schiff base of retinal isomers. J. Am. Chem. Soc. (1975)  97:2161-6. 

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

1974

Chan WK, Nakanishi K, Ebrey TG, Honig B. Letter: Properties of 14-methylretinal, 13-desmethyl-14-methylretinal, and visual pigments formed therefrom. J. Am. Chem. Soc. (1974) 96:3642-4.

Honig B, Ebrey TG. The structure and spectra of the chromophore of the visual pigments. Ann. Rev. Biophys. Bioeng. (1974) 3:151-77. 

1973

Honig B, Kabat EA, Katz L, Levinthal C, Wu TT. Model-building of neurohypophyseal hormones. J. Mol. Biol. (1973) 80:277-95. 

Honig B, Kahn P, Ebrey TG. Intrinsic optical activity of retinal isomers. Implications for the circular dichroism spectrum of rhodopsin. Biochemistry (1973) 12:1637-43. 

1972

Ebrey TG, Honig B. Ultraviolet chromophore transitions in the rhodopsin spectrum. Proc. Natl. Acad. Sci. USA (1972) 69:1897-9.

1971

Honig B, Hudson B, Sykes BD, Karplus M. Ring orientation in -ionone and retinals. Proc Natl. Acad. Sci. USA (1971) 68:1289-93.

Honig B, Karplus M. Implications of torsional potential of retinal isomers for visual excitation. Nature (1971) 229:558-60. 

1970 and earlier

Scharf B, Honig B. Comments on Vibronic Intensity Borrowing. Chem. Phys. Lett. (1970) 7:132-6.

Honig B, Jortner J. Theoretical Studies of Two Photon Absorption: II. Model Calculations. J. Chem. Phys. (1967) 47:3698-703.

Honig B, Jortner J, Szoke A. Theoretical Studies of Two Photon Absorption: I. Molecular Benzene.  J. Chem. Phys. ( 1967)46:2714-27.

Bradley DF, Lifson S, Honig B. Theory of Optical and Other Properties of Biopolymers: Applicability and Elimination of the First-Neighbor and Diople-Diople Approximations. In Electronic Aspects of Biochemistry. Academic Press, New York (1964) p.77-91.

Turner AG, Honig B, Parr RG, Hoyland JR. Off-Center Hydrogen Atom Calculations. J. Chem. Phys. (1964) 40:3216-3220.