| Accelrys Software Inc.
... develops and commercializes scientific business intelligence software for the integration, mining, analysis, modeling and simulation, management and interactive reporting of scientific data - [e] ADF
The Amsterdam Density Functional (ADF) package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers in such diverse fields as pharmacochemistry and materials science. SCM - [e] Amber
Assisted Model Building with Energy Refinement - [e] AMPAC™
... is a fully-featured semiempirical quantum mechanical program. Semichem - [e] Ascalaph
Molecular modelling software. Agile Molecule - [e] Autodock
... is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Scripps Research Institute - [e] Bio
... is a versatile tool for constructing, analyzing and minimizing molecular structures. Biographics Laboratory - [e] Biodesigner
... is a molecular modeling and visualization program for personal computers - [e] CHARMM
... is a versatile and widely used molecular simulation program with broad application to many-particle systems. Chemistry at HARvard Macromolecular Mechanics - [e] Chembrain XTE
Worldwide unique chemical database for three-dimensional molecular structures with integrated artificial intelligence capable of learning applicable in the prediction of any molecular properties as well as for use as laboratory notebook. Softonic - [d, e] Chimera
... is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF - [e] CODESSA™
... is an advanced, fully featured Quantitative Structure/Activity Relationship (QSAR) program that ties information from AMPAC™ and other Quantum Mechanics programs with experimental data. Semichem - [e] Dino
... is a realtime 3D visualization program for structural biology data - [e] g0penMol
With gOpenMol small molecules, and to lesser extent protein structures, as well as the chemical properties, total electron densities and molecule orbitals of small molecules can be visualized and analyzed.. CSC - [e] General Molecular Modeling Software
List of General Molecular Modeling (CADD, CAMM, QM, etc.) Software. NetSci - [e] GOLPE
GOLPE (Generating Optimal Linear PLS Estimations) is the state of the art chemometric toolbox for 3D QSAR. Multivariate Infometric Analysis S.r.l. - [e] GRID
... is a computational procedure for determining energetically favourable binding sites on molecules of known structure. Molecular Discovery Ltd. - [e] HyperProtein
... has a multi-window, multi-functional, project, and GUI approach to protein sequences. It creates multi-sequence alignments, phylogenetic trees and models molecular evolution. It enables studies of the relationship between protein sequence and protein structure. HyperCube, Inc. - [e] ICM
The ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. Molsoft - [e] MathMol - Mathematics and Molecules
... is designed to serve as an introductory starting point for those interested in the field of molecular modeling - [e] MidasPlus
Molecular Display and Simulation System. UCSF - [e] Molecular Modelling Toolkit, MMTK
... is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations - [e] Molecular Networks
... provides multifaceted, innovative software to the chemical, biotechnology and pharmaceutical industry. The company's suite of chemoinformatics applications covers many different areas including: handling of chemical information, design of new chemical entities and prediction of physicochemical and biological properties of chemical compounds - [e] Molgen
The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures - [e] MolScript
... is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. Avatar Software - [e] MoluCAD
... is a full-featured molecular modeling and visualization tool designed for Windows. New River Kinematics - [e] MolviZ
Molecular Visualization Resources; all free and open source, collected by Eric Martz, including all Martz-authored molecular visualization projects - [e] NAMD - Molecular Dynamics Simulator
... is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems - [e] PyMOL
... is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. DeLano Scientific LLC - [e] Raptor
... is an innovative receptor-modeling technology which is based on a novel scoring function including hydrophobicity, hydrogen bonding, entropy and the quantification of explicitly simulated induced fit. Biographics Laboratory - [e] RasMol
Molecular Visualization Freeware - [e] Raster3D
... is a set of tools for generating high quality raster images of proteins or other molecules - [e] Schrödinger
... provides accurate, reliable, and high performance computational technology to solve real-world problems in life science research - [e] Spartan
With unsurpassed visualization and a wide range of well documented computational methods in a single user-friendly software tool, Spartan delivers the full power of molecular modeling to chemists everywhere. Wavefunction, Inc. - [e] Swiss-PdbViewer
... is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface - [e] TINKER - Software Tools for Molecular Design
... is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers - [e] Vega
... was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite - [e] VMD - Molecular Graphics Viewer
... is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting - [e] Yasara
... is a molecular-graphics, -modeling and -simulation program - [e] Yeti
... is a molecular mechanics program for modeling proteins and small-molecule protein complexes. Biographics Laboratory - [e] | 
