Modeling and Simulation Software

Access additional resources of interest, submitted by community members.

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
3decision® A web-based collaborative platform that allows you to perform advanced structural analytics in an easy and fun way. Includes ligand design tools, large-scale pocket similarity search and sequence analysis.
Abalone Abalone, is a general purpose molecular modeling program focused on the dynamics of biopolymers.
AMBER AMBER (Assisted Model Building with Energy Refinement) is a molecular dynamics and energy minimization program
ANM ANM (Anisotropic network model) is a simple NMA tool for analysis of vibrational motions in molecular systems
AutoDock 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
DeepTracer DeepTracer is an automatic prediction tool for fast de novo macromolecular complex structure prediction from electron density maps
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.
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
GROMOS GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems
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
Macromoltek Molecular simulations simplified. Antibody modeling, side-chain packing, renumbering, and other web-based computational tools for antibody development available in easy-to-use workspaces. Macromoltek also provides a consulting service for customers in need of more specialized analysis.
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.
MODELLER 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.
PACKMAN: PACKing and Motion ANalysis This package focuses on studying molecular structures and their dynamics using a simple yet informative property known as Protein Packing.
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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Last updated: 2/16/2023