Software and Servers

Physics
• Machine Learning in Physics

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)

DataBases
• IGB Tools/DataBases

Systems Biology
• IGB Tools/Systems Biology
• CircadiOmics:

Software Search Engine
• Sourcerer: Database and Information Retrieval System for Source Code

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.

DeepCube: Rubik's Cube Solver
• DeepCube: A ML-based approach to solving Rubik's Cube using Deep Learning.

Please see also the IGB Tools page

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