Division of Biocomputing

Software

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

 

Chemoinformatics, molecular modeling, computational chemistry:

  • Accelrys: Accord Enterprise Informatics (AEI) and AE Inventory is the system used for UNMCMD screening informatics.  Key products in use at UNM are:
    Pipeline Pilot graphical workflow platform
    Accord Enterprise Informatics Oracle-based database system
    Accord Enterprise Inventory plugs into AEI, allows inventory and compound tracking down to wells and plates
    Accord Chemistry Engine the Oracle cartridge which provides chemical searching etc.
  • Accelrys: (legacy software) These packages are available only on SGI/IRIX and are not supported:
    Felix processing, display and analysis of NMR data
    Insight molecular design and dynamics
    Catalyst pharmacophore modeling and searching
  • AutoDock: automated docking of flexible ligands to macromolecules
  • CambridgeSoft:
    ChemDraw chemical drawing package
    ChemBioOffice database system for Windows
  • CAS Scifinder: client for Chemical Abstracts Service
  • CHARMM: macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations
  • ChemAxon
    • : wide range of chemoinformatics and molecular modeling applications and toolkits, all in Java
    Marvin Beans Marvin View, Sketch, Space
    JChem applications JKlustor, JChem Base, Standardizer, Screen, Reactor, Fragmenter, Molecular Descriptor Generator, all the calculator plugins
  • ChemNavigator: vast (~50M) 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
    3DPL docking; virtual screen iResearch libraries on client
    CncMCS max common substructure tool
    CncDiversec diverse library selection
    CncConnect client for Windows (GUI) or Linux (command-line only)
  • Dock: molecule docking, orientation and conformation searching, chemical screening
  • EduSoft: MolconnZ generates many descriptors designed for QSAR.
  • EPISuite: Free software from the U. S. Environmental Protection Agency may be downloaded, for example for computing toxicity, carcoginicity, and physical properties such as solubility, pKa and solubility.  Find information about EPA databases and software here. To download EPISuite go here. 
  • gNova: Chord is a chemical cartridge for PostgreSQL, used in the UNM Roadrunner database system
  • 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
    Chemical Virtual Classroom interactive teaching platform for chemoinformatics and biomolecular discovery
  • MOE: from Chemical Computing Group (CCG), is an extensive set of tools integrated with a powerful graphical user interface. MOE's strength is interactive 3D molecular modeling of proteins and ligands for drug discovery. However, there are also batch capabilities, 2D methods, and a web portal. MOE is well documented with a comprehensive set of hands-on tutorials, which is part of why it is an excellent for training and education. A key feature of MOE is the CCG language "SVL" (Scientific Vector Language). All methods are implemented via SVL, unifying their MOE gui and MOE/batch and MOE/web. The software runs on many platforms, including Linux(es), Windows, Mac, and Unix(es).
  • Molecular Discovery: tools for 3D descriptors, linking structure-based drug design, chemoinformatics and bioinformatics
    Tools:
    GRID molecular interaction field generation and docking
    PENGUINS virtual high throughput screening---fast library enumeration, filtering and docking
    VolSurf molecular interaction field analysis in pharmacokinetics
  • 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
  • OpenEye Scientific Software: tools that accurately quantify the shape and the electrostatics of a molecule for the purposes of lead discovery
    Tools:
    Babel molecule file format interconversion
    Filter 2D property prediction and compound selection
    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
    OEShape shape toolkit
    Vida visualization tool
    Zap Poisson-Boltzmann electrostatics scoring function
  • PyMol: PyMol is a molecular visualizer from Delano Scientific Software, 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
  • Symyx (formerly known as MDL): scientific software and databases for the life sciences
    Tools    :
    ISIS/Base database system for chemical structures
    ISIS/Draw 2D drawing of chemical structures
  • Tripos Sybyl: molecular design and dynamics
    Modules:
    SYBYL/Base includes comprehensive tools for molecular modeling: structure building, optimization, and comparison; visualization of structures and associated data; annotation, hardcopy and screen capture capabilities; and a wide range of force fields
    Advanced Computation provides a wide range of tools for conformational analysis that enumerate all possible torsional states of a molecule or identify just its low-energy conformations
    Biopolymer with FlexiDock delivers an extensive set of tools for building, visualizing, manipulating, and predicting the 3D structure of biological molecules, including proteins, peptides, nucleic acids, and polysaccharides
    Composer builds 3D models of proteins from sequence using knowledge-based homology modeling methods
    CPU  
    DISCOtech performs pharmacophore elucidation from precomputed conformations of active compounds that bind to the same target
    Dynamics  
    MatchMaker uses a threading method to predict the 3D structure of proteins from amino acid sequence
    ProTable uses SYBYL's Molecular Spreadsheet to deliver tools that analyze and assess the quality of protein structures. Graphical rendering and linked display of tabular and graphical information help communicate the results of analyse
    QSAR with CoMFA provides tools needed to build statistical and graphical models of biological activity (or other properties) from molecular structures, and to use those models in making predictions for the activity of untested compounds
    UNITY a search and analysis system for the exploration of chemical databases and features rapid, conformationally flexible 3D searching
  • 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
    Modules:
    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.

Statistical modeling, machine learning, mathematical

  • GnuPlot: data and function plotting environment, multi-platform
  • MathWorks MATLAB: matrix laboratory and visualization environment
  • R: language and environment for statistical computing and graphics
    packages:
    ROCR Receiver-Operator Characteristic curves
    drc dose-response curve generation and analysis
  • SAS: statistical analysis system
  • Umetrics: multivariate data analysis and design of experiments
    Tools:
    MODDE chemometrics design of experiments
    SIMCA-P+ chemometrics megavariate data analysis
  • WEKA: machine learning algorithms and environment for data mining tasks

 

Bioinformatics:

  • GeneSpring: statistical analysis tool for microarray data
  • ImageMaster 2-D (from GE Healthcare Life Sciences, formerly APBiotech): 2-D gel image analysis
  • PDQuest (from Bio-Rad): 2-D gels analysis software for Mac and PC

Other scientific software:

Software developed by the Division of Biocomputing:

  • Roadrunner: database system for chemical and biological data; screening and molecular discovery informatics.  Web-based user interface, built on PostgreSQL, the gNova Chord chemical cartridge, OpenEye, ChemAxon, Mesa, and other tools.  Developed for the NMMLSC (now UNMCMD) for NIH Roadmap MLI (now MLP).  Lead developer: Steve Mathias.
  • PubChem Integration Utilities: Perl and Python scripts to perform searches and integration using the PubChem User Gateway (PUG) and NCBI Entrez eUtils APIs.  These tools were developed to automate and streamline workflows involving PubChem, and avoid time consuming use of the PubChem web interface for routine and automatable tasks.

revision: 2009 May 18