Software and Data

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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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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Downloadable Software

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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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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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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