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Computational Tools and Services
List of relevant tools and services locally available at UC San Diego, San Diego Supercomputer Center or Burnham Institute.
| The Biology WorkBench - The Biology WorkBench is a revolutionary web-based tool for biologists, allowing researchers to search many popular protein and nucleic acid sequence databases. | The Molecular Information Agent (MIA) - MIA searches 50 biological databases to find all of the existing information about a query protein or DNA sequence. |
| The Protein Data Bank (PDB) - PDB is the world's central scientific repository of biological macromolecule 3-D structure data. | FPS (Family Pairwise Search) - FPS allows you to search a library of protein families with the protein sequence that you provide. Your sequence will be analyzed using the Family Pairwise Search (FPS) algorithm. [Download] |
| MEME (Multiple EM for Motif Elicitation) - The MEME system allows you to discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and, search sequence databases using motifs using MAST. The MEME system was developed by Timothy Bailey, Charles Elkan, and Bill Grundy at the UCSD Computer Science and Engineering department with input from Michael Gribskov at the San Diego Supercomputer Center. [Download] | Meta-MEME: Meta-MEME is a software toolkit for building and using motif-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences, as well as a set of motif models discovered by MEME. Meta-MEME uses this model to produce a multiple alignment of the original set of sequences and to search a sequence database for homologs. [Download] |
| Conformational Likeness Search - The Conformational Likeness Search is a method for finding 3-D similarities in protein structures from the Brookhaven Protein Databank (PDB) or from local PDB files. | CE: Combinatorial Extension of the Optimal Path is a method for finding 3-D similarities in protein structures. [Download] |
| FFAS: Fold & Function Assignment system is a profile-profile alignment method. First, PSI-Blast is used to collect homologs. Then, sequences of homologs are translated into a profile (translation is not based on PSI-Blast approach). Finally, the translated profile is aligned against a profile database. | QuickPDB: QuickPDB permits you to find and quickly review a macromolecular structure looking at interactions between sequence and structure. Typically, once you have located structure(s) of interest you would download then for further analysis using local programs. It is a view option used in the Protein Data Bank (PDB). [Download] |
| Byosinc: Structural Biology Synchrotron Users Organization. BioSync was formed in 1990 to promote access to synchrotron radiation for scientists whose primary research is in the field of structural biology. | HPSS: High Performance Storage System. SDSC provides information and daily statistics on SDSC's HPSS installation, the world's largest. Allocations of space on HPSS are available through special arrangement with SDSC. |
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