Protein structure databases
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Protein Data Bank (PDB)
Unique worldwide repository for the processing and distribution of 3-D biological macromolecular structure data..
SCOP
Structural classification of proteins - provides a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
YRC Public Data Repository (YRC PDR)
Complete proteome domain parsing, ab initio structure prediction and SCOP superfamily assignments were recently completed for the yeast Saccharomyces cerevisiae 
, and all data deposited into the YRC PDR . Additionally, all predicted structures from the on-going Human Proteome Folding project (HPF) will be deposited into this database.
PIDD is a database of Protein Inter-atomic Distance Distributions for distance based protein modeling of known protein structures such as in the Protein Data Bank (PDB). PIDD is capable of generating, caching, and displaying the statistical distributions of the distances of various types and ranges. Can be used to extract geometric restraints or mean-force potentials for protein structure determination including NMR structure determination and comparative model refinement. Users can specify distance types and ranges, and retrieve, visualize or download the results.
CKAAPs DB
Structurally-similar proteins with dissimilar sequences. The Conserved Key Amino Acid Positions DataBase ( CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases.
BMRB :: BioMagResBank
A repository for data from NMR spectroscopy of proteins, peptides and nucleic acids hosted at the University of Wisconsin, Madison.
JenaLib - Home
The goal of Jena Library of Biological Macromolecules (JenaLib) is better dissemination of information on 3D biopolymer structures, focussing on visualization and analysis. JenaLib provides access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB).
CATH is a protein domain structure database in which homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to toplogy families and homologous superfamilies are made by sequence and structure comparisons. Version 3.0 includes 86,151 classified structural domains, 1110 fold groups and 2147 homologous superfamilies. CATH Dictionary of homologous structures (CATH-DHS) contains multiple structural alignments, consensus information and functional annotations for 1459 well populated superfamilies in CATH. CATH is interlinked to Gene3D database which is a projection of CATH structural data onto ~2 million sequences in completed genomes and UniProt.
Integrated Sequence-Structure Database (ISSD)
Integrated Sequence-Structure Database Version 1.0 Level: Alpha Released: 25/06/97. Announcement (posted July 15, 2001). You can now download. ISSD Version 2.0 (4.0MB, plain text files in zip archive). It comprises non-homologous proteins ...
Decoys 'R' Us - A Database of Incorrect Protein Conformations (v1.1)
Decoys 'R' Us. Decoys are computer generated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real. The primary use of decoys is to test scoring, or energy, functions. All ...
LPFC: A Library of Protein Family Cores
A Library of Protein Family Cores. Russ Altman. Bob Schmidt. Mark Gerstein. Summary We have taken structural alignments of protein families and computed average core structures for each family. The core structures can be divided into ...
The Protein Structure Database (PSdb)
A protein database, derived from the information available in the Protein Databank and NRL-3D database.
3D-JIGSAW (version 2.0)
This server builds three-dimensional models for proteins based on homologues of known structure.
Protein Secondary Structure Database
The single worldwide repository for the secondary structural information of all known structure proteins.
SPINE :: Structure Gallery
Target Status. EBI SRS PDB. SPINE Structures Target information from the Macromolecular Structure Database (MSD) can be viewed by clicking the Target link (but access may be restricted in that database). Clicking on the PDB link will allow ...
Protein Structure and Family Data
MOE's Protein Family Database contains a set of alignments of a non-redundant set of protein structures from the PDB and protein sequences from the PIR (v67.0) database.
