A selected list of software licensed and in use at the Translational Informatics Division. Please feel free to contact us for further information.


Automated docking of flexible ligands to macromolecules


  • ChemDraw: chemical drawing package
  • ChemBioOffice: database system for Windows

CAS Scifinder

Client for Chemical Abstracts Service


Open-source cheminformatics toolkit with Java API


Wide range of chemoinformatics and molecular modeling applications and toolkits, all in Java

  • Marvin Beans: MarvinView, MarvinSketch, MarvinSpace
  • JChem applications: InstantJChem, JKlustor, JChem Base, Standardizer, Screen, Reactor, Fragmenter, Molecular Descriptor Generator, all the calculator plugins
  • JChem cartridge: Chemical cartridge for Oracle


vast (%7e50M) online chemical super-catalog, acquisition system, and search tools w/ special NIH screening center features

  • iResearch System: online search via web or Windows or Linux clients; UNM subscription via NIH/MLP
  • CncConnect: client for Windows (GUI) or Linux (command-line only)

A selected list of software licensed and in use at the Translational Informatics Division. Please feel free to contact us for further information.


Molecule docking, orientation and conformation searching, chemical screening

Golden Helix

Providing gene analytic software. Founded by Christophe Lambert, TiD Faculty.


Chord is an OpenEye-based chemical cartridge for PostgreSQL, used in the UNM Roadrunner database system.  OpenChord is open-source, OpenBabel-based.

Mesa Analytics and Computing

Tools for molecular fingerprinting and cluster analysis

  • Grouping Module: Taylor-Butina clustering with many options, able to handle large datasets
  • Fingerprint Module: fingerprint molecules based on structural keys
  • Molecular Shape Fingerprinter: Fast, storable, quasi-random grid shape + chemical features


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 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.


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


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.