Software and Data

Downloadable programs

cryoEM Refinement Tools

Programs and protocols that can be used to refine atomic structures, either experimentally determined or computationally constructed, within cryoEM density maps.

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DelPhi

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions.

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GRASP

A molecular visualization package for SGI machines ONLY which focuses on the mapping of various properties on the molecular surface. For a Windows operating system please download GRASP2. Note that there is no version for linux at this time.

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Jackal 1.5

A collection of programs designed for the modeling and analysis of protein structures.

  • scap and Sidechain Rotamer library: prediction of side-chain conformations or residue mutations. The operation can be performed on all or certain residues in one or multiple chains.
  • loopy + loopyMod: prediction of protein loop conformations or segment mutation. loopyMod used by loopBuilder.
  • nest: homology modeling.

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PrISM

An integrated computational system with tools for protein modeling and sequence and structure analysis.

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Protein-DNA Interface Alignment Software

An algorithm to perform interface alignment between any two protein-DNA complexes based on their corresponding PDB files.

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Protein-DNA Modeling Interface Software

The program can be used predict the conformation of the sidechains within a protein-DNA binding interface.

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SURFace Algorithms

Programs that calculate solvent accessible surface area and curvature corrected solvent accessible surface area. The accessible surface output is calculated for the whole molecule, per residue, and per atom.

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VISTAL

A two-dimensional visualization tool for structural alignments.

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Web-based tools

PrePPI

An on-line database of predicted and experimentally determined protein-protein interactions.

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PredUs

A tool to predict protein-protein interface based on interface conservation among structurally similar protein neighbors.

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Mark-Us

A Function Annotation Server for Protein Structures.

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OnTheFly

A database of Drosophila melanogaster transcription factors and their binding sites.

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Target Explorer

A web based tool for automatic identification of new target genes for transcription factors in the Drosophila genome.

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EDGI (Enhancer Detection using only Genomic Information)

EDGI discovers transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting.

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SCREEN

A web server tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.

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Data sets

Helix pairs

A data set of pairs of interacting helices from membrane and water-soluble proteins.

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HOMEP

A data set of homologous membrane protein structures organized into topological families, suitable for assessment of methods for alignment and homology modeling of membrane proteins.

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IAlign

Pre-computed Protein-DNA Interface Alignments.

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Supplementary materials

pKa calculations on RNA

Supplementary tables and figures accompanying our paper, "Calculation of pKa s in RNA: On the structural origins and functional roles of protonated nucleotides." in J Mol Biol. 366: 1475-96 (2007).

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