Bioinformatics & Genomics
Courses, Journals, Definitions
Portals & Comprehensive Servers
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[SRI International] The BioCyc Knowledge Library is the new name for EcoCyc and MetaCyc. It is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.
[GSF] Predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. These consensus descriptions produced by the program ConsInd consist of the length of the binding site and the individual conservation of each nucleotide position within the site.
[GSF] This program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
[UCSF] DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together.
[CuraGen] This commercial sites offers a fully integrated genomics suite of
services, including discovery-oriented software for SeqCalling with sequence and SNP data, GeneCalling with gene expression data, PathCalling with protein -protein interactions and pathways, a pharmacogenomics database of drug profiles, and SNPCalling with our database of 200,000 cSNPs (gene-based single nucleotide polymorphisms).
[Gladstone Institutes, UCSF] GenMAPP is a free computer application designed to visualize gene
expression data on maps representing biological pathways and groupings
G-Protein Coupled Receptor Database: GPCR 3D Models
[European Molecular Biology Laboratory] Database of atomic coordinates of 3D models of G-protein coupled receptors.
[NHGRI] An annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
Kyoto Encyclopedia of Genes and Genomes
[GenomeNet] "KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene
catalogs produced by genome sequencing projects."
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[Univ. College London] A program for automatically plotting protein-ligand interactions. The interactions shown are those mediated by hydrogen bonds and hydrophobic contacts.
Links to Pathway and Other Databases
[GenomeNet] A comprehensive list of links to biological and biochemical databases. The types of databases include: metabolic pathways; enzymes, compounds, and elements; regulatory pathways; protein-protein interactions; nomenclature and classification; taxonomy; and complete genomes and analysis.
Links to Pathway Databases
[Kyoto University] A list of links to databases of pathways of reactions & compounds in living cells.
[Institute for Pharmaceutical Chemistry, university of Marburg, Germany] Database system for analyzing receptor/ligand complexes deposited in the Protein Database.
[ICGEBnet] A protein domain library with structural, functional, ligand-binding, and topogenic segments of proteins.