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3-D Structure Databases
Structure Data Banks
The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), PDBe (Europe) and PDBj (Japan).
Protein Data Bank. The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures.
PDBj (Protein Data Bank Japan) maintains a centralized PDB archive of macromolecular structures.
Nucleic Acid Database, a repository of three-dimensional structural information about nucleic acids.
Biological Magnetic Resonance Data Bank's mission is to collect, archive, and disseminate the important quantitative data derived from NMR spectroscopic investigations of biological macromolecules.
Structure Resources
The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.
NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models.
PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
PDBWiki is community annotated knowledge base of biological molecular structures.
Proteopedia is a free, collaborative 3D-encyclopedia of proteins & other molecules.
DrugBank provides an analysis of the structural information available in the Protein Data Bank (PDB) relating to drug molecules and their protein targets.
Topology, Folding & Structural Classification
CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution).
The SCOP (Structural Classification of Proteins) database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
TopSearch has replaced COPS. The COPS web server is a computational tool for structural biologists that was made for the in-depth analysis of protein structures. The system covers three independent applications: qCOPS, iCOPS and ?COPS. At the heart of all three applications is the fully automated domain based protein structure classification COPS (Classification Of Protein Structures) that is weekly updated with the entries from the public repository of known protein structures (PDB).
The Dali Database is based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank* (PDB).
The Conserved Domain Database (CDD) contains protein domain models imported from outside sources, such as Pfam and SMART, and curated at NCBI. CDD content includes NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM).
Gene3D provides structural annotation for proteins in the CATH sequence databases. Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources.
Protein Topology Graph Library is a web-based database application for protein topologies.
Theoretical Models
A database of three-dimensional protein models calculated by comparative modeling.
The Protein Model Portal (PMP) gives access to the various models that can be leveraged from PSI targets and other experimental protein structures by comparative modeling methods.
The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
Specialized Databases
The Abysis antibody database integrates sequence data from Kabat, IMGT and the PDB with structural data from the PDB.
AMYPdb is an online database dedicated to amyloid precursor families and to their amino acid sequence signatures.
The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
CyBase is dedicated to the study of a fascinating new class of proteins that possess a cyclic backbone in which the N and C termini have been joined with a conventional amide bond. These recently characterised molecules have now been found in organisms from all kingdoms of life and given the current rate of discovery the number of sequences could soon number in the hundreds.
Thd CYPED database integrates information on sequence and structure of cytochrome P450 monooxygenases to facilitate protein engineering.
This database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB).
ESDTHER is dedicated to the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases.
The EyeSite database is an information and modelling resource for families of proteins that function in the eye.
The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs).
The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function.
HMRbase is a manually curated database of Hormones and their Receptors.
ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins.
Thermodynamic database for protein-nucleic acid interactions. ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids.
RNA FRABASE: an engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.
SDAP is a Web server that integrates a database of allergenic proteins with various computational tools that can assist structural biology studies related to allergens.
Protein Knots
In pKNOT, users can either submit PDB id or upload protein coordinates, it will return results about the knot type, the cores and depths of the knotted region and the protein class.
The KNOTTIN database provides standardized data on the knottin structural family.
The knot server allows the user to check pdb entries or uploaded structures for knots and to visualize them. The size of a knot is determined by deleting amino acids from both ends. This procedure is, however, not perfect and the resulting size should only be treated as a guideline.
Drug & Ligand Databases
Relibase is a database search, retrieval and analysis system for protein-ligand complex structures. Relibase+ provides easy access to all such experimental structures within the Protein Data Bank (PDB)
A database of ligand binding proteins aligned to structural templates. The structural templates are taken from the PDB
The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank.
This database provides information on hetero components included in three-dimensional biopolymer structures deposited at the Protein Data Bank (PDB) and the Nucleic Acid Database (NDB).
This database contains information about hetero-compounds encountered in files from the Protein Data Bank (PDB).
Database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.
Protein-Protein Interface Databases
Small Molecule Structure
The Cambridge Structural Database is The world repository of small molecule crystal structures.
KEGG LIGAND contains our knowledge on the universe of chemical substances and reactions that are relevant to life. It is a composite database currently consisting of COMPOUND, DRUG, GLYCAN, REACTION, RPAIR, and ENZYME databases.
A database containing over four million small organic compounds @ UC Irvine.
Empirical and theoretical structures for more than 18,000 inorganic crystals and small organic compounds.
ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 8 million purchasable compounds in ready-to-dock, 3D formats.
The Web Bench
The Web Bench
is the essential companion to the biologist, bringing informational resources and a collection of tools & calculators to facilitate work at the bench and analysis of biological data.
Check out the full online bench here
Check out the full online bench here
Sequence Analysis with GenBeans
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