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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.
  • 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.
  • 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.
  • GRASP2: A new version of GRASP for the Windows operating system (except for Vista) NOT for linux, with an enhanced GUI and new scientific tools.
  • 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.
  • PrISM: An integrated computational system with tools for protein modeling and sequence and structure analysis.
  • Protein-DNA Interface Alignment Software: An algorithm to perform interface alignment between any two protein-DNA complexes based on their corresponding PDB files.
  • Protein-DNA Modeling Interface Software: The program can be used predict the conformation of the sidechains within a protein-DNA binding interface.
  • 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.
  • VISTAL: A two-dimensional visualization tool for structural alignments.

Web based tools

  • PrePPI: An on-line database of predicted and experimentally determined protein-protein interactions. Start Server
  • PredUs: A tool to predict protein-protein interface based on interface conservation among structurally similar protein neighbors. Start Server
  • PUDGE: This protein structure prediction server provides a convenient means of integrating tools that may be used at different stages of the structural prediction process.
  • Mark-Us: A Function Annotation Server for Protein Structures.
  • OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Start Server
  • Target Explorer: A web based tool for automatic identification of new target genes for transcription factors in the Drosophila genome.
  • EDGI: (Enhancer Detection using only Genomic Information) discovers transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting.
  • STING Millennium: A web based suite of programs for comprehensive and simultaneous analysis of structure and sequence: nature and volume of atomic contacts of both intra- and inter- chain types, analysis of the quality of structure, residue conservation and its relationship with intra-chain contacts, functional parameters are also deciphered.
  • SCREEN: A web server tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.

Data sets

  • Helix pairs: A data set of pairs of interacting helices from membrane and water-soluble proteins.
  • 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.
  • IAlign: Pre-computed Protein-DNA Interface Alignments.

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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