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2nd Window 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.
[more info][14074]

2nd Window 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.
[more info][12105]

2nd Window 3D-ALI
[EMBL] A database of aligned protein structures and related sequences.
[more info][12643]

2nd Window 3DCrunch Index
[ExPASy] A database of automatically generated protein models.
[more info][12693]

2nd Window 3DInSight
[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.”
[more info][12234]

2nd Window Annotated Brookhaven Protein Database
[Bechman Institute, University of Illinois] (Shivakumar Rajaraman) Protein database for use with the Mosaic browser.
[more info][12644]

2nd Window 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.
[more info][13561]

2nd Window BioMagResBank
[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.
[more info][12309]

2nd Window BRENDA
[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.
[more info][12112]

2nd Window 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.”
[more info][12107]

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2nd Window 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.
[more info][10442]

2nd Window 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.
[more info][12649]

2nd Window 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).
[more info][12257]

2nd Window DBAli
[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.
[more info][13981]

2nd Window 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.”
[more info][12080]

2nd Window DSMP
[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.
[more info][12247]

2nd Window 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).”
[more info][12258]

2nd Window Enzyme Structures Database
[University College London] A database of the known enzyme structures in the Brookhaven Protein Data Bank.
[more info][12578]

2nd Window 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).
[more info][12652]

2nd Window 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).
[more info][12240]

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2nd Window G-Protein Coupled Receptor Database: GPCR 3D Models
[European Molecular Biology Laboratory] Database of atomic coordinates of 3D models of G-protein coupled receptors.
[more info][12653]

2nd Window 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.
[more info][13753]

2nd Window HIC-Up
[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.
[more info][12115]

2nd Window Homeodomain Resource
[NHGRI] An annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
[more info][12011]

2nd Window HOMSTRAD: Homologous Structure Alignment Database
[University of Cambridge] Database provides aligned three-dimensional structures of homologous proteins.
[more info][12656]

2nd Window 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.
[more info][12657]

2nd Window 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.
[more info][11917]

2nd Window 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.
[more info][13714]

2nd Window 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.
[more info][12660]

2nd Window 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.
[more info][12628]

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2nd Window 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.
[more info][12229]

2nd Window MedChem/Biobyte QSAR database
[MedChem/Biobyte] Database of quantitative structure-activity relationships that covers both biological and physical-organic chemistry.
[more info][12638]

2nd Window 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).
[more info][12663]

2nd Window ModBase
[Rockefeller University] Database of comparative protein structure models.
[more info][12661]

2nd Window NDB: Nucleic Acid Database
[The Nucleic Acid Database Project] This database assembles and distributes structural information about nucleic acids.
[more info][10402]

2nd Window NRL_3D Sequence-Structure Database
[Protein Information Resource] A sequence-structure database derived from the Brookhaven Protein Data Bank.
[more info][12664]

2nd Window Nucleic Acid Database
[Rutgers University] (NDB) The Nucleic Acid Database Project (NDB) assembles and distributes structural information about nucleic acids.
[more info][12111]

2nd Window OCA?
[Weizmann Institute] OCA? is a browser/database for retrieving rich content annotation on structure and function for proteins found in the Protein Data Bank.
[more info][12232]

2nd Window OLDERADO
[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.
[more info][12667]

2nd Window PClass
[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.
[more info][12246]

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