Molecular Modeling Software at BimCore

Icon Key : Homepage : Download : Kinemage : PostScript : Reference/ Manual : Graphics : Tutorial UNIX denotes that a local login to BimCore's Unix workstations is required.

Molecular Visualization Name Description Download Reference/ Manuals Tutorials/ Examples Grasp surface representations UNIX N/A N/A Midas Plus interactive graphics display for macromolecules UNIX N/A N/A Mage display and viewing of kinetic images of molecules Molscript converts molecular coordinates into B&W or color postscript (ref) Web Interface UNIX Web Rasmol manual 3D molecular graphics viewer (ref) Ribbons converts molecular coordinates into black and white postscript (ref) UNIX Sybyl biomolecular visualization, manipulation, building, design, and analysis (ref) contact Tripos UNIX N/A View visualization and calculation program UNIX N/A N/A

Homology Modelling Name Description Download Reference/ Manuals Tutorials/ Examples Composer, Sybyl comparative structural modelling, T. Blundell contact Tripos UNIX N/A Matchmaker, Sybyl inverse folding, tertiary structure prediction, J. Skolnick contact Tripos UNIX N/A N/A Modeller structural modelling, A. Sali (ref) Web Interface UNIX Web ProFit structural modelling by fold recognition, M. Sippl UNIX N/A N/A Threader sequence to structure alignment (ref) Web Interface Web N/A

Protein Analysis Name Description Download Reference/ Manuals Tutorials/ Examples Contact Script Calculates residue surface area in contact between two protein molecules. N/A Probe Probe reads in PDB files and outputs a file that highlights contacts dots for use in a kinamage, O, or XtalView file. It also quantifies packing information such as vdw, h-bonds, and atomic bumping in a score table. (ref) Web Interface Web ProCheck Checks include geometrical and conformational analysis such as dehedral angles, chirality, h-bonds, and a residue-by-residue analysis. Part of Biotech Validation Suite for Protein Structures with ProCheck V3.5, Prove V2.3, and What If V4.99. Web Interface UNIX Web Profiler3D geometrical and conformational analysis UNIX N/A N/A Prosa II PROtein Struture Analysis program to measure energetic aspects of protein structures. The program yields an overall quality score to determine native/non-native folds as well as graphs showing problematic areas.Readme file Derivatives: ProFIT and SuperPos. License required, demo available. N/A ProTable, Sybyl Interactive Spreadsheet for Sophisticated Analysis of Protein Structures contact Tripos UNIX N/A N/A Reduce Adds hydrogens onto PDB coordinate files - this is helpful to run before using Probe, which considers all atoms. Probe results will be more accurate using Reduce. N/A WhatIF WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.” Overview (ReadMe) Derivatives: WHAT_CHECK (provides more and different checks than ProCheck, which manly checks geometry), WHAT_DIGIT UNIX

Interactive Protein Design Name Description Download Reference/ Manuals Tutorials/ Examples Sculpt interactive molecular docking and minimization UNIX N/A N/A Sybyl biomolecular manipulation, building, design, and analysis (ref) contact Tripos UNIX N/A

Protein-Protein Docking & Drug Design Name Description (*see a longer decription of each) Download Reference/ Manuals Tutorials/ Examples Macromodel Software in collaboration with Emerson Center conformational search and molecular dynamic simulations N/A Ours Theirs Coming AutoDock* Flexible: automated docking of flexible ligands to macromolecules N/A N/A Dock* Rigid: locates feasible binding locations Web Interface UNIX Web N/A Escher* Rigid: protein docking, can be applied to protein reconstruction N/A N/A Gramm* Rigid: protein docking N/A N/A Sculpt interactive molecular docking and minimization UNIX N/A VMD visual molecular dynamics N/A N/A N/A Sybyl Specific Docking Programs: FlexiDock, SiteID, FlexX, CScore, LeapFrog (ref) UNIX N/A N/A

For more docking programs, please see this page.

Crystallographic Structure Determination Name Description Download Reference/ Manuals Tutorials/ Examples CCP4 package of crystallographic software tools UNIX N/A N/A CNS a flexible multi-level hierarchical approach for the most commonly used algorithms in macromolecular structure determination UNIX N/A N/A Merlot molecular replacement program UNIX N/A N/A O molecular modelling and manipulation, electron density visualization UNIX N/A Phases generation of electron density maps UNIX Rave Large Software Package UNIX N/A N/A SHARP a computer program for macromolecular crystallography UNIX N/A N/A TNT crystallographic data refinement package N/A N/A N/A Xplor crystallographic data refinement package UNIX N/A N/A Xtal View visual protein crystallographic software system UNIX N/A N/A