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Bioinformatics & Genomics
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Proteins & Other Biological Molecules
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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.
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.”
Berkeley Sequence and Structure Search Site
[University of California, Berkeley] Computational biology site dedicated to aiding biomolecular sequence and structure searching. Along with selected database-searching resources, site offers advice for sequence searching.
[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.”
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.
Database of Macromolecular Movements
[Gerstein Lab, Yale University] A database with associated tools for geometric analysis that describes the motions that occur in proteins and other macromolecules, particularly using animations and movies.
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).
[Laboratories of Molecular Biophysics, Rockefeller University] DBAli is a database that includes approximately 35,000 alignments of pairs of protein structures from SCOP and CE. DBAli islinked to several resources, including Compare3D and ModView for visualizing sequence alignments and structuresuperpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets ofalignments suitable for benchmarking sequence-sequence and sequence-structure alignment methods under a variety ofconditions.
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.”
[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.
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).
G-Protein Coupled Receptor Database: GPCR 3D Models
[European Molecular Biology Laboratory] Database of atomic coordinates of 3D models of G-protein coupled receptors.
Hetero-compound Information Centre
[Uppsala University] This site contains information about hetero-compounds (small molecules) encountered in files from theProtein Data Bank. The HIC-Up database contains output from the program HETZE which attempts to check the quality ofhetero-compounds, and a list of other hetero-compounds which are either identical to the present compoundor a superstructure of it.
[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.
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.
Image Library of Biological Macromolecules
[IMB Jena] The JENA library provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). It is aimed at a better dissemination of information on three-dimensionalbiopolymer structures with an emphasis on visualization and analysis.
Indiana University Molecular Structure Center
[Indiana University] X-ray crystallography educational resource. The Indiana University Molecular Structure Center is a laboratory specializes in the structural determination of smallmolecules.
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.
LSU rRNA database
[Departement Biochemie, Universiteit Antwerpen] A database on the structure of large ribosomal subunit RNA including indications of secondary structure elements for each sequence.
Macromolecular Structure Database
[EBI] “The EBI Macromolecular Structure Database is the European Project for the collection, management, anddistribution of data about macromolecular structures.” This database includes the PDB and other structures/databases.
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).
[Sutcliff Group, University of Leicester, UK] Database of core atoms, domains, and representative structures from all current NMR-derived protein structures deposited in the PDB. Includes on-site analysis tools.
[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.
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