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Bioinformatics & Genomics
3-D Structure Prediction
Protein Data Bank (PDB)
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Secondary Structure Prediction & Assignment
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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.
[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.”
The ASTRAL Compendium for Sequence and Structure Analysis provides databases and tools useful for analyzing protein structures and their sequences. It is partially derived from, and augments the SCOP: Structural Classification of Proteins database. Most of the resources provided here depend upon the coordinate files maintained and distributed by the Protein Data Bank.
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.
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.
[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.
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.
[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.
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.
[Analytical Biostatistics Section – NIH] “FORESST is a database (with search engine) of hidden Markov models that characterize secondary structure representations of protein structural domains.”
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.
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.
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.
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.
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.
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).
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).
[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.
Protein Data Bank
[Research Collaboratory for Structural Bioinformatics] The PDB is the single international repository for the processing and distribution of 3-D macromolecularstructure data primarily determined experimentally by X-ray crystallography and NMR. This is an indispensable resource for structural biology, especially proteins.
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.
RESID: Database of Modified Amino Acids
[Protein Information Resource] A database of protein covalent structural modifications with descriptive, chemical, and bibliographic information.
[Fox Chase Cancer Center] S2C is a database correlating sequence and atomic coordinate residue numbering in the Protein Data Bank. It contains files correlating the implicit residue numbering in the SEQRES records of a PDB file with the numbering found in the ATOM (coordinate) records. A FASTA formatted version of the PDB amino acide sequences is also provided.