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http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

•   Source: SciCrunch Registry

http://www.thesgc.org/

Charity registered in United Kingdom whose mission is to accelerate research in new areas of human biology and drug discovery.Not for profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on large scale and cost effectively targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.

Proper citation: Structural Genomics Consortium (RRID:SCR_003890) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/enzymes/

Database of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them.

Proper citation: Enzyme Structures Database (RRID:SCR_007125) Copy   

•   Source: SciCrunch Registry

http://biodev.cea.fr/interevol/

InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface

Proper citation: InterEvol database (RRID:SCR_006054) Copy   

•   Source: SciCrunch Registry

http://restraintsgrid.bmrb.wisc.edu/NRG/MRGridServlet

Original NMR (nuclear magnetic resonance) data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED) respectively as described in the references. There are 9,672,968 parsed constraints in 7159 entries. (Mar. 2013)

Proper citation: NMR Restraints Grid (RRID:SCR_006127) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbsum

Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.

Proper citation: PDBsum (RRID:SCR_006511) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

•   Source: SciCrunch Registry

http://consurfdb.tau.ac.il/

Provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB. Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles.

Proper citation: ConSurf Database (RRID:SCR_002320) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/

Portal of glycoinformatics resources including databases and bioinformatics tools for glycobiology and glycomics research. Databases include a bibliography, structure, nuclear magnetic resonance (NMR), mass spectroscopy (ms) and a PDB search.

Proper citation: glycosciences.de (RRID:SCR_002324) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/tools/pdb2linucs/

Service that automatically extracts carbohydrate information from pdb-files and displays it in LINUCS or IUPAC notation. Many pdb-files contain carbohydrate structures. Since there is not such a standard nomenclature like it exists for amino acids, it is difficult to find the carbohydrate information. Sometimes entire oligosaccharides are encoded in one single residue. Information about carbohydrate linkages is often missing, and if it is present, it is not in a unique format and therefore also difficult to find.

Proper citation: pdb2linucs (RRID:SCR_001566) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.charite.de/synsysnet/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication.

Proper citation: SynSysNet (RRID:SCR_003180) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/protein

Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Proper citation: NCBI Protein Database (RRID:SCR_003257) Copy   

•   Source: SciCrunch Registry

http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/

Protein Data Bank (PDB) contains data on the spatial protein structures and their biologically active sites (i.e., ligand binding regions, enzyme catalytic centers, regions subjected to biochemical modifications, etc.). However, neither of the well known systems searching PDB does not provide the user with possibility to make the queries related with the active sites. A database PDBSITE storing the data on biologically active sites contained in the PDB database has been developed. PDBSITE accumulates amino acid content, structure features calculated by spatial protein structures, and physicochemical properties of sites and their spatial surroundings.

Proper citation: Protein Data Bank Site (RRID:SCR_008227) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/database/start.php?action=form_pdb_data

Search for carbohydrate containing PDB entries by criteria like species or the compound / classification terms. You can choose predefined, frequent terms from the pull-down-menus or enter your own queries manually.

Proper citation: pdb-data (RRID:SCR_000386) Copy   

•   Source: SciCrunch Registry

http://crdd.osdd.net/raghava/ccpdb/

ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible.

Proper citation: ccPDB - Compilation and Creation of datasets from PDB (RRID:SCR_005870) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/emdb/

Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

Proper citation: Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) Copy   

•   Source: SciCrunch Registry

https://cansar.icr.ac.uk/

canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data.

Proper citation: canSAR (RRID:SCR_006794) Copy   

•   Source: SciCrunch Registry

http://www.emdataresource.org/

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

Proper citation: EMDataResource.org (RRID:SCR_003207) Copy   

•   Source: SciCrunch Registry

http://www.pdbj.org/

PDBj (Protein Data Bank Japan) maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU.

Proper citation: PDBj - Protein Data Bank Japan (RRID:SCR_008912) Copy   

•   Source: SciCrunch Registry