Bioinformatics & Genomics
Cell Biology & Metabolism
Gene Expression & Information
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 and
reactivity of each molecule. This large amount of information provides a better quality resource for the user.
[EMBL] A database of aligned protein structures and related sequences.
[ExPASy] A database of automatically generated protein models.
[Institute of Physical and Chemical Research] "3DInSight is an integrated database and search tool for structure, property, and function of biomolecules, which will help
researchers to get insight into their relationship."
Annotated Brookhaven Protein Database
[Bechman Institute, University of Illinois] (Shivakumar Rajaraman) Protein database for use with the Mosaic browser.
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."
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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 is
linked to several resources, including Compare3D and ModView for visualizing sequence alignments and structure
superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of
alignments suitable for benchmarking sequence-sequence and sequence-structure alignment methods under a variety of
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 a
resolution 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.
DSSP Source Code
[CMBI] "The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)."
Enzyme Structures Database
[University College London] A database of the known enzyme structures in the Brookhaven Protein Data Bank.
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).
FSSP ftp Site
[EBI] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
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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 the
Protein Data Bank. The HIC-Up database contains output from the program HETZE which attempts to check the quality of
hetero-compounds, and a list of other hetero-compounds which are either identical to the present compound
or a superstructure of it.
[Uppsala University] The Hetero-compound Information
Centre - Uppsala is a freely-accessible resource for structural biologists dealing with
hetero-compounds ("small molecules") encountered in files from the Protein Data Bank.
[NHGRI] An annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
HOMSTRAD: Homologous Structure Alignment Database
[University of Cambridge] Database provides aligned three-dimensional structures of homologous proteins.
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-dimensional
biopolymer 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 small
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.
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Macromolecular Structure Database
[EBI] "The EBI Macromolecular Structure Database is the European Project for the collection, management, and
distribution of data about macromolecular structures." This database includes the PDB and other structures/databases.
MedChem/Biobyte QSAR database
[MedChem/Biobyte] Database of quantitative structure-activity relationships that covers both biological and physical-organic chemistry.
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).
[Rockefeller University] Database of comparative protein structure models.
NDB: Nucleic Acid Database
[The Nucleic Acid Database Project] This database assembles and distributes structural information about nucleic acids.
NRL_3D Sequence-Structure Database
[Protein Information Resource] A sequence-structure database derived from the Brookhaven Protein Data Bank.
Nucleic Acid Database
[Rutgers University] (NDB) The Nucleic Acid Database Project (NDB) assembles and distributes structural information about nucleic acids.
[Weizmann Institute] OCAŠ is a browser/database for retrieving rich content annotation on structure and function for proteins found in the Protein Data Bank.
[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 from
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Protein Data Bank
[Research Collaboratory for Structural Bioinformatics] The PDB is the single international repository for the processing and distribution of 3-D macromolecular
structure 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.
Protein Topology Home Page
[EBI] This site offers services devoted to protein structural topology and protein topology cartoons.
[Institute for Pharmaceutical Chemistry, university of Marburg, Germany] Database system for analyzing receptor/ligand complexes deposited in the Protein Database.
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.
[ICGEBnet] A protein domain library with structural, functional, ligand-binding, and topogenic segments of proteins.
SCOP: Structural Classification of Proteins
[MRC Laboratory of Molecular Biology and Centre for Protein Engineering] Survey of known protein folds; information on close relatives of a given protein using keywords and homology searches.
SRPDB: Signal Recognition Particle Database
[Univ of Texas Health Center] Provides annotated SRP RNA sequences from eukaryotes and archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make available representative RNA secondary structure diagrams where each base pair is proven by comparative sequence analysis.
SSU rRNA database
[Departement Biochemie, Universiteit Antwerpen] A database on the structure of small ribosomal subunit RNA including indications of secondary structure elements for each sequence.
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[The Nucleic Acid Database Project] A search of macromolecular structure databases developed by the NDB Project using a quick or full search.
tmRDB: tmRNA Database
[University of Texas Health Center] A database on the structures and functions of the tmRNA (earlier called "10S RNA"). The database provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements.
TOPS: Protein Structural Topology
[European Bioinformatics Institute] This server allows searches of the TOPS database of topological patterns in protein structures.
[University of Texas Health Center at Tyler] A tool in the study of the structures and functions of various uRNA's that provides aligned, annotated, and phylogenetically ordered sequences.
Web-Based Bioinformatics Databases
[Systems Integration for Manufacturing Applications] The purpose of this project is to create two databases that can evaluate structures and interactions of macromolecules. The first database characterizes the recognition by one molecule of a reaction site to another and the second database involves the effort of the macromolecular structure data bank.