Bioinformatics & Genomics
Cell Biology & Metabolism
Gene Expression & Information
Proteins & Other Biological Molecules
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3D Virtual Chemistry Library
[Imperial College of Science, Technology & Medicine] A molecular database that includes structure in several formats, physical data, history and
reactivity of each molecule. This large amount of information provides a better quality resource for the user.
[Institute of Physical and Chemical Research] "3DInSight is an integrated database and search tool for structure, property, and function of biomolecules, which will help
researchers to get insight into their relationship."
[Univ. of Wisconsin] "A Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Amino Acids." The database includes information on each biological molecule, NMR spectral parameters, kinetics, thermodynamics,and structure.
[EBI] This enzyme database contains information about nomenclature, reaction and specificity, enzyme structure, isolation/preparation, stability, literature references, and cross references to sequence and 3D-structure data banks.
Cambridge Structural Database
[Univ. of Cambridge] "The Cambridge Structural Database (CSD) contains crystal structure information for over 220,000 organic and metal organic compounds. All of these crystal structures have been analyzed using X-ray or neutron diffraction techniques."
Center for Advanced Research in Biotechnology
[University of Maryland and the National Institute of Standards and Technology] Joint government/university research site. Includes research and graduate study opportunities, a biological macromolecular crystallization database, and TkRaster3D.
[San Diego Supercomputer Center] The Conserved Key Amino Acid Positions database provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. CKAAP database provides CKAAPs of the representative set of proteins derived from the Combinatorial Extension algorithm and FSSP databases.
Clusters of Orthologous Groups
[NCBI] (COGs) A phylogenetic database (with a comparison search server incorporated) of orthologous proteins in many complete genomes.
Danish Centre for Human Genome Research
[The Danish Biotechnology Programme, the Danich Cancer Society and The Danish Centre for Molecular Ge] Developer of the 2-D PAGE databases for functional genome analysis in health and disease emphasizing global cell regulation, skin biology and bladder cancer. The databases contain data on proteins identified in various reference maps. Users can display protein names and information on specific protein spots. Also has 2-D gel image gallery.
Directory of P450-containing Systems
[Degtyarenko and Fabian] The goal of this WWW directory is to facilitate access to electronic resources world wide for all researchers working in the field of P450 proteins and P450-containing systems.
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DNA Binding Protein Structural Families
[Univ. College London] "These Web pages include a structural classification of all protein-DNA complexes solved by X-ray crystallography to a
resolution of 3.0 angstroms or better as of 4th January 2000."
[Gis Infobiogen, Gracy/Argos] A database of homologous protein domain families obtained from successive sequence analysis steps including similarity search, domain delineation, multiple sequence alignment, and motif construction.
[Centre for DNA Fingerprinting and Diagnostics] The Database of Structural Motifs in Proteins contains a representative protein data set derived using the PDB_SELECT program, where 1351 chains with 228325 residues were obtained using a 25% threshold on the PDB release 2000 and all the proteins in the PDB.
EF-Hand Calcium-Binding Proteins Data Library
[Vanderbilt University] The EF-Hand Calcium-Binding Proteins Data Library is a growing collection of published sequence, structural, functional, and other
information about EF-hand calcium-binding proteins and their roles in cellular signal transduction.
[ExPASy at the Swiss Institute of Bioinformatics] An enzyme nomenclature database based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB).
Enzyme Structures Database
[University College London] A database of the known enzyme structures in the Brookhaven Protein Data Bank.
[Argonne National Laboratories] The EMP database contains detailed information on a very large number of enzymes from over 17,000 articles. It can be searched by name, EC number, taxon, tissue, or organelle.
[AGRO and INRA] A database containing information on the molecular forms, promoters, gene structures, mutations, mutalign, and a variety of tables on cholinesterases and related enzymes.
Finding 3-D Similarity in Protein Structures
[San Diego Supercomputing Center] This site provides two methods for comparing 3D protein structures, and structure neighbor databases derived from them. Combinatorial Extension (CE) determines an optimal alignment between aligned fragment pairs (AFPs). AFPs are
determined from local geometry averaged over 8 C alpha positions. Heuristics are used to prevent a combinatorial
explosion. Final alignments are by dynamic programming. Compound Likeness (CL) uses a probabalistic approach to comparing a wide variety of properties.
[Uppsala University] The Hetero-compound Information
Centre - Uppsala is a freely-accessible resource for structural biologists dealing with
hetero-compounds ("small molecules") encountered in files from the Protein Data Bank.
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HIV Protease Database
[The National Cancer Institute] An archive of experimentally determined 3-D structures of Human Immunodeficieny Virus 1 (HIV-1), Human Immunodeficieny Virus 2 (HIV-2), and Simian Immunodeficiency Virus (SIV) proteases and their complexes.
[NHGRI] An annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
[Weizmann Institute of Science, Genome and Bioinformatics, Isreal] Contains many different types of information about proteins and other biologically active molecules (e.g. lipids, carbohydrates, and gases) that may be promising targets for medical applications.
ICN: Ion Channel Network
[University of Leicester, and the Center for Neuroscientific Databases at the University of Minnesota] Information on ion channel genes and proteins.
IMGT: International ImMunoGeneTics Database
[Universite Montpellier II] An integrated database specializing in Immunoglobulins, T-cell receptors, and major histocompatibility, and MHC/HLA-DB . An IMGT tool, DNAPLOT, will allow Ig, TcR, and MHC sequence analysis.
Klotho: Biochemical Compounds Declarative Database
[Institute for Biomedical Computing, Washington University] This database was developed as a beginning attempt to model biological processes. It catalogues biochemical compounds and their properties.
LIGAND: Ligand Chemical Database for Enzyme Reactions and Chemical Compounds
[Kyoto University] Provides linkage between chemical and biological aspects in enzymatic reactions. The database consists of three sections: the ENZYME section, the COMPOUND section, and the REACTION section.
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.
[Ohio State University] A relational database of thermodynamic and associated information on lipid mesophase and crystal polymorphic transitions. Database includes lipid molecular structures.
The Live Bench Project is a continuous
benchmarking program. Every week new Protein Data Bank (PDB)
proteins are submitted to all participating
fold recognition servers. The results are
collected and evaluated using automated model
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[Babraham Institute] A database of peptidases, provding a catalogue and structure-based classification.
Metabolism & Biocompounds Resources
[University of Nebraska, Lincoln] Links to metabolism, metabolic pathway and biocompound databases and information resources.
[University of Minnesota] MetaFam is a comprehensive database of protein family information. This site contains functional assigments for
protein sequences and indicates the confidence of each assignment by
showing how all the other family databases have made the classification.
Molecules R US
[NIH] A WWW Forms interface which facilitates access (browsing, searching and retrieval) to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB).
Nucleic Acid Database
[Rutgers University] (NDB) The Nucleic Acid Database Project (NDB) assembles and distributes structural information about nucleic acids.
[Weizmann Institute] OCAŠ is a browser/database for retrieving rich content annotation on structure and function for proteins found in the Protein Data Bank.
[Center for Biological Sequence Analysis] Database of O-glycosylated proteins. Site also includes a version of the database which contains no identical O-glycosylation sites for prediction purposes.
[Stanford University] A protein structure classification tool that ranks an input protein using its PDB file in a heirarchical classification of 600 representative structures from
[Birkbeck College, London] A database which gives each sequence giving the name, sequence, and references peptaibol sequences where atomic coordinates are available, diagrams are given for peptaibols.
[Washington University, St. Louis] Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains based on the Swissprot 38 and SP-TrEMBL 11 protein sequence databases.
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Pfam ftp Site
[Washington University, St. Louis] The ftp site for downloading the Pfam protein domain database and the associated tools.
PKR: Protein Kinase Resource
[San Diego Supercomputing Center] A web accessible compendium of information on the protein kinase family of enzymes. This resource includes tools for structural and computational analyses and links.
[Berkeley University] PRESAGE is a collaborative resource for protein structure. It provides a database of proteins, each of which has a collection of annotations reflecting current experimental status, structural assignments models, and suggestions.
PRINTS: Protein Fingerprint Database
[University of Manchester] "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used
to characterise a protein family; its diagnostic power is refined by iterative scanning of a
[Research Computing, Protein Information Resource] A non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
ProDom: The Protein Domain Database
[INRA] "The ProDom protein domain database consists of an automatic compilation of homologous domains."
ProNIT is a thermodynamic database for Protein-Nucleic Acid Interactions, which play important roles in the regulation of gene expression. Experimental interaction data provide valuable information for understanding the protein-nucleic
[ExPASy] A searchable dictionary of proteins and patterns. Identifies to which family of proteins a sequence belongs.
Protein Disease Database
[NIMH-NCI] Database for correlating diseases with proteins observable in serum, CSF, urine and other common human body fluids.
Protein Structure Database
[Pittsburgh Supercomputing Center] (PSdb) A new protein database that relates secondary (e.g. Helix, Sheet, Turn, Random Coil), supersecondary (e.g. helix-helix interactions), and tertiary information (e.g. Solvent accessibility, internal relative distances, and ligand interactions) to the primary structure. The data for each protein is supplied on a residue by residue basis and encoded in a series of flat ASCII files.
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[Munich Information Center for Protein Sequences] ProtFam by MIPS is a curated protein classification database. In a joint effort, MIPS and
PIR-NBRF classify sequences into
superfamilies and families and annotate homology domains. This is part of the joint project to
produce the PIR-International Protein Sequence Database.
REBASE: The Restriction Enzyme Database
[New England BioLabs] (Richard Roberts and Dana Macelis) Information on restriction enzymes, methylases, the organisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, availability, and reference material.
RNA Modification Database
[Univ. of Utah] A comprehensive list of post-transcriptionally modified nucleotides from RNA.
[ICGEBnet] A protein domain library with structural, functional, ligand-binding, and topogenic segments of proteins.
[ExPASy at the Swiss Institute of Bioinformatics] Data on proteins identified on various 2-D PAGE reference maps.
[ExPASy at the Swiss Institute of Bioinformatics] A database of high quality imagery of biological macromolecules with known three-dimensional structure.
Worthington Enzyme Manual
[Worthington Biochemical Corp.] A database of information on enzymes and related biochemicals.