University of California, Irvine (UCI)
School of Information and Computer Sciences (ICS)
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.

© 2017 Pierre Baldi | pfbaldi [at] uci [dot] edu