Public Domain Molecular Modeling SoftwareĪ parallel object-oriented molecular dynamics simulation program Supports membrane patches and vesicles, microdomains as well as stacking of monolayer and/or bilayer membranes.Ī program for automated protein homology modeling Interactively generate heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement. 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 Macromoltek also provides a consulting service for customers in need of more specialized analysis. Antibody modeling, side-chain packing, renumbering, and other web-based computational tools for antibody development available in easy-to-use workspaces. Cornell Theory Center program for potential optimization and alignments of sequences and structures Linear Optimization of Protein Potentials.
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MolSoft ICM programs and modules for applications including for structure analysis, modeling, docking, homology modeling and virtual ligand screening GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems 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.Ĭomplete modelling package for proteins, membrane systems and more, including fast molecular dynamics, normal mode analysis, essential dynamics analysis and many trajectory analysis utilities
JMOL SIMULATION FREE
Free for academics.ĪMBER (Assisted Model Building with Energy Refinement) is a molecular dynamics and energy minimization programĪNM (Anisotropic Network Model)ANM (Anisotropic network model) is a simple NMA tool for analysis of vibrational motions in molecular systemsĪ suite of automated docking tools designed to predict how small molecules, such as substrate or drug candidates, bind to a receptor of known 3D structureĬHARMM (Chemistry at HARvard Molecular Mechanics) is a molecular dynamics and energy minimization programĭeepTracer is an automatic prediction tool for fast de novo macromolecular complex structure prediction from electron density mapsĪnalyze the flexibility in molecular structures of any size, Quickly explore the available conformational space of the input moleculeĪ program for carrying out rigid-body docking between biomolecules Includes ligand design tools, large-scale pocket similarity search and sequence analysis.Ībalone, is a general purpose molecular modeling program focused on the dynamics of biopolymers.Īffinity, a free energy function for estimating binding affinities. 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 refinementĪ web-based collaborative platform that allows you to perform advanced structural analytics in an easy and fun way. Biologically Interesting Molecule Reference Dictionary (BIRD)Īccess user-submitted suggestions of websites related to macromolecular structure.