Proteins & Other Biological Molecules
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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 andreactivity 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 helpresearchers 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.
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.
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 aresolution 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 otherinformation 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).
[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 aredetermined from local geometry averaged over 8 C alpha positions. Heuristics are used to prevent a combinatorialexplosion. 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 InformationCentre – Uppsala is a freely-accessible resource for structural biologists dealing withhetero-compounds (“small molecules”) encountered in files from the Protein Data Bank.
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.
[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.
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 continuousbenchmarking program. Every week new Protein Data Bank (PDB)proteins are submitted to all participatingfold recognition servers. The results arecollected and evaluated using automated modelassessment programs.
[University of Minnesota] MetaFam is a comprehensive database of protein family information. This site contains functional assigments forprotein sequences and indicates the confidence of each assignment byshowing 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).
[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 fromthe PDB.
[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.