123D A program which threads a sequence through a set of structures using substitution matrix, secondary structure prediction and contact capacity potential
Affinity Affinity, a free energy function for estimating binding affinities. Free for academics.
AMBER AMBER (Assisted Model Building with Energy Refinement) is a molecular dynamics and energy minimization program
Animations Animations - a PDB viewer with an educational point of view. Includes animated simulator to view molecule forces on a picometer distance scale and an attometer time scale.
ANM ANM (Anisotropic Network Model)ANM (Anisotropic network model) is a simple NMA tool for analysis of vibrational motions in molecular systems
AutoDock3.0
A suite of automated docking tools designed to predict how small molecules, such as substrate or drug candidates, bind to a receptor of known 3D structure
CHARMM CHARMM (Chemistry at HARvard Molecular Mechanics) is a molecular dynamics and energy minimization program
Disulfide by Design
An application for the rational design of disulfide bonds in proteins and for exporting mutant PDB files containing the modeled disulfides for visualization in other molecular modeling software, for Windows
3D-DOCK Suite Includes - FTDock which performs rigid-body docking between biomolecules; RPScore which uses a pair potentials to screen output from FTDock; and MultiDock which performs multiple copy side-chain refinement
FIRST Analyze the flexibility in molecular structures of any size, Quickly explore the available conformational space of the input molecule
FTDOCK A program for carrying out rigid-body docking between biomolecules
GNM GNM (Gaussian Network Model): oGNM calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.
GROMOS GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems
GROMACS Complete modelling package for proteins, membrane systems and more, including fast molecular dynamics, normal mode analysis, essential dynamics analysis and many trajectory analysis utilities
ICM MolSoft ICM programs and modules for applications including for structure analysis, modeling, docking, homology modeling and virtual ligand screening
LOOPP Linear Optimization of Protein Potentials. Cornell Theory Center program for potential optimization and alignments of sequences and structures
MAMMOTH
MAtching Molecular Models Obtained from THeory - a program for automated pairwise and multiple structural alignments; for SGI, Linux, and Sun Solaris
MidasPlus A program for displaying, manipulating and analysing macromolecules
MCCE
Multi-Conformation Continuum Electrostatics software: Calculates theoretical pKas of residues in proteins and provides the modulating factors of pKas based on the structure in PDB format
MODELLER A program for automated protein homology modeling
MOIL Cornell Theory Center package for molecular dynamics simulation of biological molecules
NAMD A parallel object-oriented molecular dynamics simulation program
YASARA A complete molecular graphics and modeling program, including interactive molecular dynamics simulations, structure determination, analysis and prediction, docking, movies and eLearning for Windows, Linux and MacOSX.
ZMM
An Internal Coordinate Molecular Modeling Program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of torsion angles, bond angles, bond lengths, positions of free molecules and ions, and orientation of free molecules. ZMM includes a Graphical User Interface (MVM).
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