Multivariate Infometric Analysis Srl

Software for chemometric analysis with specialty tools to analyze, manipulate and transform molecular fields. Many of the tools are useful in 3D-QSAR, pharmacodynamic optimization, and diverse fields of drug design and development. A list of their products is available.

NMRPipe

Processing, display and analysis of NMR data

OpenBabel

An open-source toolkit with C++ and Python APIs.

OpenEye Scientific Software

Tools that accurately quantify the shape and the electrostatics of a molecule for the purposes of lead discovery

  • Brood: bioisostere search for lead optimization
  • FRED: Fast Rigid Exhaustive Docking
  • OEChem: cheminformatics toolkit with C++, Python and Java APIs
  • Omega: rapid multiple-conformer generation
  • ROCS: shape similarity and database search
  • Vida: visualization tool

PyMol

PyMol is a molecular visualizer now managed by Schrodinger, which allows free use of PyMol for educational purposes only. Our current license does not permit research use. PyMol is available for windows, mac and linux.

RasMol

Graphical display of tertiary structures by Roger Sayle

RDKit

Open-source cheminformatics and machine learning toolkit with C++ and Python APIs

VMD

Visual Molecular Dynamics, a free and open-source package from the NIH Resource for Macromolecular Modeling and Bioinformatics, University of Illinois at Champaign-Urbana

VxInsight

Tool for discovering relationships within large databases

Xcalibur

Universal mass spectrometry data system

  • Protein ID: protein database
  • TurboSEQUEST: protein identification

WebMO

A web interface to several computational chemistry packages (quantum, ab initio, semi-empirical). Packages currently available:

  • Tinker:
  • : a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
  • GAMESS: Quantum chemistry computation system.
  • MOPAC: general-purpose semiempirical molecular orbital package for the study of solid state and molecular structures and reactions
  • NWChem: many  methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. In addition, NWChem has the capability to perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.