University of California, Irvine (UCI)
School of Information and Computer Sciences (ICS)
Center for Machine Learning and Intelligent Systems (CML)
  Institute for Genomics and Bioinformatics (IGB)
 
Software

Software and Servers

 

Physics | Chemoinformatics | Structural Proteomics | Functional Proteomics | Genomics
DataBases | Systems Biology | Software Search Engine | Virtual World

 


    Chemoinformatics
  • ChemDB:
    Chemoinformatics portal including:
    1. A large database (5M) of organic compounds for molecular docking, drug screening, and retrosynthesis applications;
    2. Multiple Web server predictors of physical, chemical, and biological properties;
    3. An organic chemistry expert system (Reaction Explorer) used to power several applications, such as Synthesis Explorer and Mechanism Explorer. Synthesis Explorer and Mechanism Explorer are interactive tutorial systems to learn undergraduate-level organic chemistry. Synthesis Explorer and Mechanism Explorer have been adopted and are currently used in all relevant undergraduate organic chemistry classes at UCI.

    Structural Proteomics (SCRATCH suite)
  • SSpro: Protein secondary structure prediction server (3 classes)
  • SSpro8: Protein secondary structure prediction server (8 classes)
  • ACCpro: Solvent accessibility prediction server
  • CONpro: Residue contact number prediction server
  • DIpro: Disulphide bridge prediction server
  • MUpro: Single amino acid mutation stability prediction server
  • DISpro: Disordered region prediction server
  • DOMpro: Domain prediction server
  • BETApro: Prediction of beta-residue and beta-strand pairings.
  • CMAPpro: Contact map prediction server
  • FOLDpro: Prediction of protein tertiary structure (Fold Recognition).
  • CCMAPpro: Coarse contact map prediction server
  • CMAP23Dpro: 3D reconstruction from contact map
  • 3Dpro: 3D structure prediction server
  • ICBS: Inter-chain beta sheet database of protein-protein interactions
  • TMBpro: Prediction of transmembrane beta-barrel features and tertiary structure.
  • SVMcon: Prediction of amino acid contact maps using Support Vector Machines.
  • SELECTpro: Protein model selection using a structure-based energy function.
  • SOLpro: Prediction of protein solubility.
  • SIDEpro: Prediction of protein side-chain conformations.
  • ANTIGENpro: Prediction of protein antigenicity.
  • BEpro: B-cell epitope prediction server.
  • COBEpro: B-cell continuous epitorpe prediction server.

    Functional Proteomics
  • HMMpro:
    Hidden Markov Model simulator for biological sequence analysis, with graphical interface
    Available upon request, please contact pfbaldi [at] uci [dot] edu
  • Link Finder: Processes mass spectrometry data and allows users to identify peptides linked by MS cleavable crosslinkers.

    Genomics
  • MotifMap: Genomewide maps of regulatory motifs
  • Cyber-T: DNA microarray gene expression analysis server
  • LineUp: Comparative genomics server
  • CloseUp: Comparative genomics server
  • PPDB: Poxvirus Proteomics database
  • HMMpro:
    Hidden Markov Model simulator for biological sequence analysis, with graphical interface
    Available upon request, please contact pfbaldi [at] uci [dot] edu
  • DSSB:
    DNA Structure Sequence Browser
    Available upon request, please contact pfbaldi [at] uci [dot] edu
  • GOnet:
    Yeast database and visualization tool combining gene (SGD), gene ontology (GO), and gene interaction (GRID) information
  • Sigmoid Database: Database for molecular interactions and pathways (Systems Biology)




    Virtual World
  • Universal Campus: The Universal Campus provides an infrastructure for organizing and deploying collaborative meetings, such as classes, research group meetings, and conferences in a virtual 3D world.

 

Please see also the IGB Tools page

To license any of these tools, please contact pfbaldi [at] uci [dot] edu.

© 2022 Pierre Baldi | pfbaldi [at] uci [dot] edu