Modeling and Simulation Software Links

  • Abalone
    Abalone, is a general purpose molecular modeling program focused on the dynamics of biopolymers.
  • Affinity
    Affinity, a free energy function for estimating binding affinities. Free for academics.
    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 (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
    Analyze the flexibility in molecular structures of any size, Quickly explore the available conformational space of the input molecule
    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 is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems
    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
    Linear Optimization of Protein Potentials. Cornell Theory Center program for potential optimization and alignments of sequences and structures
  • 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
  • MembraneEditor
    Interactively generate heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement. Supports membrane patches and vesicles, microdomains as well as stacking of monolayer and/or bilayer membranes.
    A program for automated protein homology modeling
  • MOIL
    Public Domain Molecular Modeling Software
  • NAMD
    A parallel object-oriented molecular dynamics simulation program
  • OpenContact
    OpenContact is an open source, PC software tool for quickly mapping the energetically dominant atom-atom interactions between chains or domains of a given protein. A simple GUI is provided to the user to perform the mapping and no knowledge of the underlying programs are required. Output files to the user are in the form of color graphics, spreadsheets, and text files.
  • WAM - Web Antibody Modelling
    A server for automated structure modeling from antibody Fv sequences
    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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