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Sort by Program
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Description
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Contact
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Sort by Operating System
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Crystallography
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ACMI
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Automatic Crystallographic Map Interpretation
ACMI is a suite of programs designed to automate construction of a macromolecular model from an electron density map. It is specifically developed to handle low-resolution (3-4 Angstrom resolution) and poorly phased electron density maps.
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Janet Finer-Moore
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PC Linux
(charybdis & raxis4 only)
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AMoRe
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Stand alone molecular replacement package
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Pascal Egea
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IRIX, PC Linux
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ARP/wARP 7.0.1 
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ARP/wARP , is a program package for protein structure refinement. On-line Manual
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PC Linux, OSF/1, IRIX, MacOSX
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AutoDock 4
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Automated Docking of Flexible Ligands to Receptors
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Chris Waddling
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Alpha Linux, IRIX, IRIX64, OSF1, and MacOSX
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Babel 1.6
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Interconvert a number of file formats currently used in molecular modeling.
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Chris Waddling
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Alpha Linux, IRIX, IRIX64, and MacOSX
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| BnP 1.02 |
A combination of SnB & Phases:
SnB: A dual-space, direct-methods procedure for determination of MIR and MAD heavy atom substructure.
Phases: derivative refinement and some density leveling. |
NO CONTACT
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PC Linux and MacOSX
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AutoBuster
BDG
Buster
Gelly
MakeTNT |
autoBUSTER is a framework and collection of tools, intended for refining structures with the latest version of the BUSTER-TNT refinement program in conjunction with the geometry module GELLY and the restraints toolbox MakeTNT. |
NO CONTACT
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PC Linux and MacOSX
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CCP4_6.1.1
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A large collection of programs that covers everything from data reduction to refinement (Tutorial)
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NO CONTACT
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Alpha Linux, IRIX, PC Linux, OSF/1 & MacOS X (Fink)
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CNS_1.2
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Phasing and refinement program with many useful utilities
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Luke Rice
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Alpha Linux, PC Linux, IRIX, OSF/1 & MacOSX
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Denzo 1.97.9
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Data reduction, integration, merging and scaling of X-ray data
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Chris Waddling
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PC Linux, OSF/1 & IRIX
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| Dock 6.2 |
DOCK addresses the problem of "docking" molecules to each other. |
NO CONTACT
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PC Linux
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DockEM
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Quantitatively dock, or fit, a crystal structure into an EM map of a molecular compelx that contains that structure
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Peter Hwang
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OSF/1
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EPMR v8.03
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EPMR is a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. (Manual PDF)
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Frank Hays
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Alpha Linux, PC Linux, OSF/1 & IRIX
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Escet 0.6b
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A script driven program to analyse and compare three-dimensional protein structures
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HKL2000
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Data reduction, integration, merging and scaling of X-ray data |
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PC Linux, OSF/1 & IRIX
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| HOLE2 |
HOLE allows the visualization and analysis of the holes through atomic models of ion channels |
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PC Linux and IRIX
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LaueView
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Use for data processing of Laue Frames as an alternative to the CCP4 Laue Program Suite
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Pinar Erciyas
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IRIX
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Main
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MAIN is an interactively driven computer program dealing with computational parts of macromolecular crystallography in progressively automated manner
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Mead
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MEAD is a set of software objects for the purpose of modeling the electrostatics of molecules
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| MIFit |
MIFit is a fitting and molecular modeling program (Manual PDF) |
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PC Linux
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| Modeller 9v5 |
A Program for Protein Structure Modeling |
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PC Linux, MacOSX, IRIX
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Mosflm 7.0.1
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Data reduction, integration of X-ray data
Bug for Mosflm & SCALA
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Chris Waddling
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Alpha Linux, IRIX, PC Linux, OSF/1 & MacOSX
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MSMS v2.5.5
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Molecular Surfaces Computation
User Commands
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Pascal Egea
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MacOSX
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Muscle
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MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences.
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PC Linux, MacOSX (Fink)
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NAMD
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NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
User Guide v2.5b1
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Neema Salimi
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Alpha Linux, MacOSX
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PHASER-2.1.4
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Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods
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IRIX, PC Linux, OSF1, & MacOSX
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PHASES
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Bill Furey's program for derivative refinement and some density leveling.
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OSF/1 & IRIX
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| Phenix-1.4-3 |
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Pascal Egea
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IRIX, PC Linux
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SHARP
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Heavy atom refinement program.
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Chris Waddling
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Alpha Linux & IRIX
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SHELX-97
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Refinement using structure factor summation-mainly for use with high resolution data
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Chris Waddling
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Alpha Linux, PC Linux, IRIX, OSF/1 & MacOSX
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SnB v2.3
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A dual-space, direct-methods procedure for determination of MIR and MAD heavy atom substructure.
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NO CONTACT
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IRIX, OSF/1
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Solve-2.13 &
ReSolve-2.13
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Automated crystollagraphic structure solution for MIR and MAD-locate heavy atoms, calculate phases.
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NO CONTACT
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Alpha Linux, IRIX, PC Linux, OSF/1 & MacOS X
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Vega 2.2.0
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Creates a bridge between most of the molecular software packages
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| XDS |
X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. |
Earl Rutenber
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IRIX, PC Linux, and MacOSX
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xplor
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Model refinement
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Neema Salimi
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Alpha Linux, IRIX & OFS/1
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| SAXS |
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| Bunch 8.0 |
Domain structure determination of multidomain proteins against multiple SAXS data sets. |
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PC Linux, MacOSX
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| Crysol 2.6 |
A program to evaluate X-ray solution scattering of biological macromolecules from their atomic coordinates |
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PC Linux, MacOSX
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| Cryson 2.6 |
A program to evaluate neutron solution scattering of biological macromolecules from their atomic coordinates |
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PC Linux, MacOSX
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| Dammin 5.3 |
Ab inito shape determination by simulated annealing using a single phase dummy atoms model |
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PC Linux, MacOSX
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| Damaver 3.1 |
This is a set of programs to align the models provided by DAMMIN and GASBOR and to build "the most probable" model. |
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PC Linux, MacOSX
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| Gasbor 2.2 |
Ab inito reconstruction of a protein structure by a chain-like ensemble of dummy residues |
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PC Linux, MacOSX
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| GNOM 4.5 |
Small-Angle Scattering Data Processing by Means of the Regularization Technique |
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PC Linux, MacOSX
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| Sasref 7 |
Quaternary structure determination of multisubunit complexes by rigid body modelling against SAXS and SANS data. |
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PC Linux, MacOSX
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| Situs 2.3 |
Situs is a program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. The software supports both rigid-body and flexible docking using a variety of fitting strategies. |
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MacOSX, PC Linux
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| Supcomb |
Using SAXS data, superimposes one 3D structure onto another |
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PC Linux, MacOSX
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