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3 Dee – Database of Protein Domain Definitions
[European Bioinformatics Institute] 3Dee contains structural domain definitions for all protein chains in the Protein Databank (PDB) [EBI-MSD/RCSB] that have 20 or more residues and are not theoretical models.
[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.
CAME: Center of Applied Molecular Engineering
[Institute of Chemistry and Biochemistry, University of Salzburg] CAME offers a variety of internet services such as: a protein structure superimposition server [ProSup], the structural genome annotation for C. elegans [WILMA], and a protein structure analysis tool [PROSAII].
CATH Protein Structure Classification
[Univ. College, London] A novel hierarchical classification of protein domain structures, which clusters proteins at four levels: class, architecture, topology, and homologous superfamily.
CMS Molecular Biology Resource
[San Diego Supercomputer Center] A compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Moldeling.
Database of Secondary Structure in Proteins
[EBI] (DSSP) The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
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.
[National Center for Biotechnology Information] Provides a General search for nucleotide sequences, protein sequences, biomolecule 3D structures, genomes, taxonomy or literature.
FSSP: Fold classification based on Structure-Structure alignment of Proteins
[European Molecular Biology Laboratory] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
GeneFIND: Gene Family Identification Network Design
[Protein Information Resource] A database search system combining search/alignment tools and the ProClass database. Output includes global and motif scores, alignments to the best-matched members of the Pro-Site protein groups and PIR superfamilies, motif pattern matches, and links to the corresponding ProClass family records.
[European Bioinformatics Institute] “GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases.”
[Gladstone Institutes, UCSF] GenMAPP is a free computer application designed to visualize geneexpression data on maps representing biological pathways and groupingsof genes.
G-Protein Coupled Receptor Database: GPCR 3D Models
[European Molecular Biology Laboratory] Database of atomic coordinates of 3D models of G-protein coupled receptors.
HSSP: Homology-derived Secondary Structure of Proteins
[EMBL] A database of homology-derived secondary structure of proteins created by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile.
LAMA: Local Alignment of Multiple Alignments
[Fred Hutchinson Cancer Research Center] This program compares multiple protein sequence alignments with each other. The program can search databases of such multiple alignments. The search is for sequence similarities between conserved regions of protein families.
Library of Protein Family Cores
[The Helix Group at Stanford University] A library useful for building models, threading, and exploring analysis. Contains structural alignments of protein families and computed average core structures for each family.
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.
MMDB: Molecular Modeling Database
[Entrez at NCBI] A compilation of all the Brookhaven Protein Data Bank 3-dimensional structures of biomolecules from crystallographic and NMR studies. Structures in MMDB have been compared with one another using VAST (Vector Alignment Search Tool).
Molecular Sequence Megaclassification
[Washington Univ., St. Louis] Provides access to a non-redundant molecular sequence collection that can be accessed by domain type of sequence.
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).
PDB at a Glance
[National Institutes of Health] PDB At A Glance consists of a set of pre-defined biochemically meaningful search contexts (accessed by keyword) that represent the entire territory of the database.
[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.
PIR – International Protein Sequence Database
[Protein Information Resource] A database containing information concerning all naturally occurring wild-type proteins, of which the primary structure is known.
PRINTS BLAST Search
[University of Manchester] “This is an interface to a BLAST search of all protein sequences contained within the PRINTS database. The user entered sequence may be a protein or DNA sequence.”