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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Resource Report Resource Website 10000+ mentions |
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) | RCSB PDB | database, data or information resource, service resource, storage service resource, data repository | 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. | 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list |
is used by: Structural Genomics Consortium is used by: Ligand Expo is used by: DARC - Database for Aligned Ribosomal Complexes is used by: FireDB is used by: Protein Data Bank Bind Database is used by: Protein Data Bank Site is used by: NIF Data Federation is used by: ChannelPedia is used by: MobiDB is used by: BALBES is used by: Structural Antibody Database is used by: BioLiP is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is affiliated with: EMDataResource.org is affiliated with: ConSurf Database is related to: pdb-data is related to: PDB2MultiGif is related to: GlyProt is related to: pdb-care is related to: pdb2linucs is related to: GlyVicinity is related to: GlyTorsion is related to: GlySeq is related to: AffinDB is related to: StatAlign is related to: Community Structure-Activity Resource is related to: Binding MOAD is related to: ConSurf Database is related to: glycosciences.de is related to: DOMINE: Database of Protein Interactions is related to: Jenalib: Jena Library of Biological Macromolecules is related to: SynSysNet is related to: EMDataResource.org is related to: PDBe - Protein Data Bank in Europe is related to: TFinDIT is related to: HOLLOW is related to: ccPDB - Compilation and Creation of datasets from PDB is related to: DOMMINO - Database Of MacroMolecular INteractiOns is related to: InterEvol database is related to: Polbase is related to: PoSSuM is related to: ProtChemSI is related to: RNA CoSSMos is related to: PDBsum is related to: Worldwide Protein Data Bank (wwPDB) is related to: canSAR is related to: CAPS Database is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is related to: Combinatorial Extension (CE) is related to: Metalloprotein Site Database is related to: PDBj - Protein Data Bank Japan is related to: Statistical Torsional Angles Potentials of NMR Refinement Database is related to: Metalloprotein Ligand Interaction Database is related to: CARP is related to: PDBTM is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE is related to: AmiGO is related to: ConsensusPathDB is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: FlyMine is related to: NCBI Protein Database is related to: NCBI Nucleotide is related to: FunTree is related to: IndelFR - Indel Flanking Region Database is related to: NMR Restraints Grid is related to: Enzyme Structures Database is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI) is related to: Worldwide Protein Data Bank (wwPDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: MINAS - Metal Ions in Nucleic AcidS is related to: PDBj - Protein Data Bank Japan has parent organization: University of California at San Diego; California; USA has parent organization: Rutgers University; New Jersey; USA is parent organization of: RCSB PDB Software Tools is parent organization of: Protein Data Bank Markup Language is parent organization of: Ligand Expo works with: CellPhoneDB |
NIH ; DOE ; NSF DBI-1338415 |
PMID:12037327 | Public, Acknowledgement requested | nif-0000-00135, SCR_017379, r3d100010327 | http://www.rcsb.org, http://www.pdb.org, | http://www.rcsb.org/pdb/ | SCR_012820 | RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank | 2026-08-09 09:06:01 | 12459 | |||
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RCSB PDB Software Tools Resource Report Resource Website 1+ mentions |
RCSB PDB Software Tools (RRID:SCR_000035) | portal, data or information resource, software resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools. | Information Portal, Biological Macromolecular Structure, RCSB, RCSB software tools, data extraction, format conversion, data parsing, data management, visualization, pdbx/mmcif, pdbx, mmcif |
is listed by: LabWorm is related to: Protein Data Bank Markup Language has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31399 | SCR_000035 | RCSB Software Tools | 2026-08-09 09:02:53 | 2 | ||||||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | data or information resource, narrative resource, markup language, standard specification, interchange format | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-08-09 09:04:06 | 2 | ||||||
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Ligand Expo Resource Report Resource Website |
Ligand Expo (RRID:SCR_006636) | database, data or information resource, resource | 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. | element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS ; NIDDK |
PMID:15059838 | nif-0000-21237, OMICS_02751 | http://ligand-depot.rutgers.edu/ | SCR_006636 | Ligand Depot | 2026-08-09 09:04:33 | 0 | ||||||
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Enzyme Structures Database Resource Report Resource Website 1+ mentions |
Enzyme Structures Database (RRID:SCR_007125) | EC->PDB, EC-PDB | database, data or information resource, image collection | 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. | enzyme, structure, gold standard |
is related to: PDBsum is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute |
Wellcome Trust | nlx_30980 | SCR_007125 | 2026-08-08 11:58:54 | 3 | ||||||||
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NMR Restraints Grid Resource Report Resource Website |
NMR Restraints Grid (RRID:SCR_006127) | NMR Restraints Grid | database, data or information resource, image collection | 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) | nmr, biomolecule, structure, magnetic resonance, database of converted restraint, filtered restraints database, fred, mri, protein, nucleic acid |
is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Biological Magnetic Resonance Data Bank (BMRB) |
European Union FP6 contract QLG2-CT-2000-01313; NLM LM05799 |
PMID:12766409 PMID:16041478 |
Please acknowledge the references in publications where the data from this site have been utilized. | nlx_151606 | SCR_006127 | BMRB NMR Restraints Grid | 2026-08-08 11:58:41 | 0 | |||||
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ConSurf Database Resource Report Resource Website 100+ mentions |
ConSurf Database (RRID:SCR_002320) | ConSurfDB | database, data or information resource, service resource | 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. | PDB, Protein DataBase, evolution, conservation, protein, structure, pre-calculated, profile, FASEB list |
is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Tel Aviv University; Ramat Aviv; Israel | PMID:20478830 PMID:15980475 PMID:12499312 PMID:11243830 |
Free, Freely available | nif-0000-21098, SCR_007609, BioTools:consurf-db, nif-0000-02685 | http://bental.tau.ac.il/new_ConSurfDB/, https://bio.tools/consurf-db | http://consurf-hssp.tau.ac.il | SCR_002320 | , consurf-db, ConSurf-DataBase, ConSurf-DB, ConSurfDB, ConSurf Server Database, ConSurfDataBase, ConSurf- Data Base | 2026-08-08 11:57:40 | 318 | |||
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National Library of Medicine Resource Report Resource Website 100+ mentions |
National Library of Medicine (RRID:SCR_011446) | NLM | government granting agency | NLM collects, organizes, and makes available biomedical science information to scientists, health professionals, and the public. The Library's Web-based databases, including PubMed/Medline and MedlinePlus, are used extensively around the world. NLM conducts and supports research in biomedical communications; creates information resources for molecular biology, biotechnology, toxicology, and environmental health; and provides grant and contract support for training, medical library resources, and biomedical informatics and communications research. Celebrating its 175th anniversary in 2011, the National Library of Medicine (NLM), in Bethesda, Maryland, is a part of the National Institutes of Health, U.S. Department of Health and Human Services (HHS). Since its founding in 1836 as the library of the U.S. Army Surgeon General, NLM has played a pivotal role in translating biomedical research into practice. It is the world's largest biomedical library and the developer of electronic information services that deliver trillions of bytes of data to millions of users every day. Scientists, health professionals, and the public in the United States and around the globe search the Library's online information resources more than 1 billion times each year. The Library is open to all and has many services and resources for scientists, health professionals, historians, and the general public. NLM has over 17 million books, journals, manuscripts, audiovisuals, and other forms of medical information on its shelves, making it the largest health-science library in the world. In today's increasingly digital world, NLM carries out its mission of enabling biomedical research, supporting health care and public health, and promoting healthy behavior by: * Acquiring, organizing, and preserving the world's scholarly biomedical literature; * Providing access to biomedical and health information across the country in partnership with the 5,800-member National Network of Libraries of Medicine (NN/LM); * Serving as a leading global resource for building, curating and providing sophisticated access to molecular biology and genomic information, including those from the Human Genome Project and NIH Common Fund; * Creating high-quality information services relevant to toxicology and environmental health, health services research, and public health; * Conducting research and development on biomedical communications systems, methods, technologies, and networks and information dissemination and utilization among health professionals, patients, and the general public; * Funding advanced biomedical informatics research and serving as the primary supporter of pre- and post-doctoral research training in biomedical informatics at 18 U.S. universities. |
is used by: DisGeNET recommends: Brain Image Library recommends: Data Archive BRAIN Initiative recommends: OpenNeuro recommends: Brain Observatory Storage Service and Database (BossDB) recommends: CRCNS recommends: NCBI database of Genotypes and Phenotypes (dbGap) recommends: NIMH Data Archive recommends: ENCODE recommends: Genotype-Tissue Expression recommends: HMP Data Analysis and Coordination Center recommends: Illuminating the Druggable Genome recommends: Kids First Data Resource Portal recommends: HMS LINCS Database recommends: Metabolomics Workbench recommends: Patient-Reported Outcomes Measurement Information System recommends: Cancer Nanotechnology Laboratory (caNanoLab) recommends: Cancer Imaging Archive (TCIA) recommends: Network Data Exchange (NDEx) recommends: eyeGENE recommends: National Eye Institute (NEI) Commons recommends: National Sleep Research Resource (NSRR) recommends: CardioVascular Research Grid (CVRG) recommends: AMP-AD Knowledge Portal recommends: National Archive of Computerized Data on Aging (NACDA) recommends: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) recommends: Immune Tolerance Network TrialShare recommends: The Immunology Database and Analysis Portal (ImmPort) recommends: VectorBase recommends: Virus Pathogen Resource (ViPR) recommends: LONI Image and Data Archive recommends: NeuroImaging Tools and Resources Collaboratory (NITRC) recommends: Child Language Data Exchange System (CHILDES) recommends: Data and Specimen Hub (NICHD DASH) recommends: National Children's Study (NCS) Archive recommends: PhonBank recommends: Archive of Data on Disability to Enable Policy (ADDEP) recommends: National Addiction and HIV Data Archive Program (NAHDAP) recommends: Neuroscience Information Framework recommends: National Institute on Drug Abuse Center for Genetic Studies recommends: NIDA Data Share recommends: AphasiaBank recommends: FluencyBank recommends: NIDDK Central Repository recommends: NIDDK Information Network (dkNET) recommends: Nuclear Receptor Signaling Atlas recommends: Chemical Effects in Biological Systems (CEBS) recommends: Cell Image Library (CIL) recommends: PhysioNet recommends: Transporter Classification Database recommends: Biological General Repository for Interaction Datasets (BioGRID) recommends: Federal Interagency Traumatic Brain Injury Research Informatics System recommends: NeuroMorpho.Org recommends: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) recommends: The NINDS Human Cell and Data Repository (NHCDR) recommends: ClinicalTrials.gov recommends: dbSNP recommends: dbVar recommends: GenBank recommends: Gene Expression Omnibus (GEO) recommends: NCBI Sequence Read Archive (SRA) recommends: 1000 Functional Connectomes Project recommends: exRNA Atlas recommends: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) recommends: PeptideAtlas recommends: Zebrafish Information Network (ZFIN) recommends: FlyBase recommends: Database of Interacting Proteins (DIP) recommends: Mouse Genome Informatics (MGI) recommends: UniProt recommends: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) recommends: European Nucleotide Archive (ENA) recommends: Analysis, Visualization, and Informatics Lab-space (AnVIL) recommends: DNA DataBank of Japan (DDBJ) recommends: UniProtKB recommends: SPARC Portal is related to: CureHunter is related to: Entrez has parent organization: National Institutes of Health is parent organization of: MalariaWorld is parent organization of: GenNav is parent organization of: NIH Common Data Element Repository is parent organization of: MEDLINE is parent organization of: ClinicalTrials.gov is parent organization of: Developmental and Reproductive Toxicology Database is parent organization of: Directory of Health Organizations Online is parent organization of: Haz-Map: Occupational Exposure to Hazardous Agents is parent organization of: Hazardous Substances Data Bank is parent organization of: Drug Information Portal is parent organization of: NIH Data Sharing Repositories is parent organization of: MeSH is parent organization of: Unified Medical Language System is parent organization of: NCBI is parent organization of: MedlinePlus is parent organization of: RxNorm is parent organization of: Bibliography on Alternatives to the Use of Live Vertebrates in Biomedical Research and Testing is parent organization of: Chemical Carcinogenesis Research Information System is parent organization of: International Toxicity Estimates for Risk is parent organization of: BLAST Assembled RefSeq Genomes is parent organization of: Cross-Sectional and Longitudinal Aging Study is parent organization of: OrbitProject is parent organization of: Household Products Database is parent organization of: Entrez Utilities is parent organization of: Epidemiology of Chronic Disease in the Oldest Old |
nlx_inv_1005117 | SCR_011446 | U.S. National Library of Medicine | 2026-08-08 11:59:51 | 412 | |||||||||
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PDB2MultiGif Resource Report Resource Website |
PDB2MultiGif (RRID:SCR_001489) | web application, software resource | A web tool that takes a 3D structure (a PDB input file) and generates an animated image which can be displayed using any browser without the need for any additional molecular visualization software. | visualization, 3d structure, chemical structure, animation, 3d spatial image, molecule, modeling, molecular visualization |
is listed by: glycosciences.de is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Giessen; Hesse; Germany |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152874 | http://www.dkfz-heidelberg.de/spec/pdb2mgif/ | SCR_001489 | PDB to MultiGIF | 2026-08-08 12:02:40 | 0 | |||||||
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HOLLOW Resource Report Resource Website 10+ mentions |
HOLLOW (RRID:SCR_005729) | HOLLOW | software resource, software application, data visualization software, data processing software | HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets. | surface image, protein, protein image, protein structure, image, channel surface, electrostatic surface, interior pathway surface, ligand-binding surface, molecular structure, python |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
Center for Membrane Protein Structure ; Membrane Protein Expression Center ; Howard Hughes Medical Institute |
PMID:19014592 | nlx_149186 | SCR_005729 | HOLLOW - Volume Filling of Protein Structures, HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures | 2026-08-08 12:02:53 | 37 | ||||||
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DOMMINO - Database Of MacroMolecular INteractiOns Resource Report Resource Website 1+ mentions |
DOMMINO - Database Of MacroMolecular INteractiOns (RRID:SCR_005958) | DOMMINO | database, data or information resource | DOMMINO is a comprehensive structural database on macromolecular interactions. As of June, 2011, it contains more than 407,000 binary interactions. The distinctive features of DOMMINO are: # Automated updates: DOMMINO is fully automated and is designed to update itself on a weekly basis, one day after a PDB weekly update. Thus, the community will be able to study macromolecular interactions almost immediately after they are released by PDB. # Coverage of non-domain mediated interactions: In addition to domain-domain and domain-peptide interactions the database characterizes the interaction between domains and unstructured protein regions that are not parts of a domain, such as inter-domain linkers and N- and C-termini. The interactions that involve the latter unstructured parts of proteins have been included to the database for the first time providing additional ~186,000 interactions (~45% of the total number of interactions, as of June, 2011). # Coverage of new structural domains: DOMMINO employs one of the most accurate structural classifications of proteins, SCOP. In addition to the existing SCOP-annotated domains, we employ a state-of-the-art machine learning approach to classify newer protein structures into existing SCOP families. With the progress of structural genomics, we do not expect a significant growth of the number of structurally novel folds or protein families and therefore our method allows covering almost all new protein structures. In total, using this predictive approach has allowed us to add more than 261,000 new interactions, almost twice as many as existing SCOP-annotated interactions. # The web-interface is designed to give the user a possibility of a flexible search as well as the capability to study macromolecular interactions in a PDB structure at the interaction network level and at the individual interface level. The web interface of the DOMMINO database includes a comprehensive list of help topics linked to the specific actions. In addition, we have designed a step-by-step tutorial that covers all aspects of working with the data from DOMMINO using the web interface. | macromolecular interaction, macromolecule, structural domain, non-domain mediated interaction, protein, domain, peptide, interaction, protein-protein interaction, protein-peptide interaction, protein-dna interactions, protein-rna interactions, rna-rna interactions, rna-dna interactions, interface structure, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: SCOP: Structural Classification of Proteins has parent organization: University of Missouri; Missouri; USA |
NSF DBI-0845196 | PMID:22135305 | biotools:dommino, nlx_151316 | http://orion.rnet.missouri.edu/~nz953/DOMMINO/, https://bio.tools/dommino | SCR_005958 | Database Of MacroMolecular INteractiOns | 2026-08-08 12:04:06 | 1 | |||||
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ProtChemSI Resource Report Resource Website 1+ mentions |
ProtChemSI (RRID:SCR_006115) | ProtChemSI | database, data or information resource | The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly. | protein, chemical, 3d structure, biological network, interaction, ligand, prediction, fasta, fasta sequence, smiles string, complex, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
PMID:21573205 | Acknowledgement requested | nlx_151590, biotools:protchemsi | https://bio.tools/protchemsi | SCR_006115 | Protein-Chemical Structural Interactions, ProtChemSI: protein-chemical interaction database, ProtChemSI - the database of protein-chemical structural interactions | 2026-08-08 12:04:02 | 3 | |||||
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SynSysNet Resource Report Resource Website 1+ mentions |
SynSysNet (RRID:SCR_003180) | SynSysNet | database, data or information resource | 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. | gene, synapse, protein, interaction, compound, disease, structure, model, compound, protein-drug interaction, protein-protein interaction, pathway, drug-target, small molecule, interaction network, homology, drug, drug-target interaction, compound-protein interaction, visualization, proteomics, network |
is listed by: OMICtools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
Huntington's disease, Chorea Huntington, Epilepsy, Multiple Sclerosis, Parkinson's disease, Schizophrenia, Neurological disease | European Union Seventh FPSYNSYS 242167; DFG GRK1772; DFG GRK1360 |
PMID:23143269 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156893, OMICS_01914 | SCR_003180 | SynSysNet - Synaptic Proteins Database | 2026-08-08 12:03:43 | 3 | ||||
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NCBI Protein Database Resource Report Resource Website 1000+ mentions |
NCBI Protein Database (RRID:SCR_003257) | NCBI_GP, NCBI Protein, NCBI GP | database, data or information resource | 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. | amino acid sequence, nucleotide, dna sequence, protein, sequence, sequence data, structure, function, dna, nucleotide sequence, genomics, protein binding, gold standard |
is used by: NIF Data Federation is listed by: re3data.org is related to: AmiGO is related to: GenBank is related to: RefSeq is related to: TPA is related to: UniProtKB is related to: Protein Information Resource is related to: Protein Research Foundation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BioExtract is related to: DIG IT - Database of Immunoglobulins and Integrated Tools has parent organization: NCBI |
Free, Freely available | SCR_017486, r3d100011331, nif-0000-03178 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein, https://doi.org/10.17616/R3JH0X | SCR_003257 | Entrez Protein, Protein Database, NCBI Protein Database, Protein sequence database, Entrez Protein Database | 2026-08-08 12:03:43 | 1025 | ||||||
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NCBI Nucleotide Resource Report Resource Website 100+ mentions |
NCBI Nucleotide (RRID:SCR_004860) | NCBI Nucleotide, NCBI gi | database, data or information resource | Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. | gene expression, genomics, nucleic acid, biological assay, nucleotide, gold standard |
is listed by: re3data.org is related to: GenBank is related to: BioExtract is related to: DIG IT - Database of Immunoglobulins and Integrated Tools is related to: RefSeq is related to: TPA is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: NCBI |
nlx_84100, r3d100010778 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore, http://www.ncbi.nlm.nih.gov/nuccore, https://doi.org/10.17616/R3NG8J | SCR_004860 | Nucleotide Database, Entrez Nucleotide, CoreNucleotide, Nucleotide | 2026-08-08 12:03:49 | 378 | |||||||
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PDBTM Resource Report Resource Website 50+ mentions |
PDBTM (RRID:SCR_011962) | PDBTM | database, data or information resource | Comprehensive and continuously updated transmembrane protein database of the Protein Data Bank (PDB) created by scanning all PDB entries with the TMDET algorithm. Resource for transmembrane proteins and their structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list |
is listed by: OMICtools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: TMDET has parent organization: Hungarian Academy of Sciences; Budapest; Hungary works with: CCTOP |
Hungarian Scientific Research Fund ; Hungarian Academy of Sciences |
PMID:23203988 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01613 | SCR_011962 | PDBTM, Protein Data Bank of Transmembrane Proteins | 2026-08-08 12:04:29 | 51 | |||||
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MINAS - Metal Ions in Nucleic AcidS Resource Report Resource Website 1+ mentions |
MINAS - Metal Ions in Nucleic AcidS (RRID:SCR_013145) | MINAS | database, data or information resource | Database compiling the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 A radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids. | metal ion, binding pocket, nucleic acid, metal-ligand distance, innersphere ligand, outersphere ligand, ligand, element, functional group, residue, protein databank, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: Nucleic Acid Database is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Zurich; Zurich; Switzerland |
Swiss National Science Foundation PP002-68733/1 | PMID:22096233 | nlx_151459, biotools:minas | https://bio.tools/minas | SCR_013145 | Metal Ions in Nucleic AcidS, MINAS - A Database of Metal Ions in Nucleic AcidS | 2026-08-08 12:04:31 | 5 | |||||
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Protein Data Bank Bind Database Resource Report Resource Website 1+ mentions |
Protein Data Bank Bind Database (RRID:SCR_008224) | PDBBIND Database | database, data or information resource | A database of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). The PDBbind database is a collection of the experimentally measured binding affinities exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). It thus provides a link between energetic and structural information of those complexes and may be of great value to various molecular recognition studies. This site was last updated in 2007. The updated version of the resource is maintained by the Shanghai Institute of Organic Chemistry (http://www.pdbbind.org.cn). | energetic, affinity, atom, bind, bond, ligand, model, molecular, molecule, protein, structural, type |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is used by: Drug Design Data Resource |
University of Michigan; Michigan; USA ; Office of the Vice President of Research |
nif-0000-21314 | SCR_008224 | Protein DataBank Bind Database | 2026-08-08 12:04:21 | 2 | |||||||
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Protein Data Bank Site Resource Report Resource Website 1+ mentions |
Protein Data Bank Site (RRID:SCR_008227) | PDBSITE | database, data or information resource | 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. | enzyme, functional, active, activity, amino acid, binding, biochemical, biological, biologically, biology, biotechnology, catalytic, dna, heterocomplex, inorganic, interaction, ligand, medicine, modification, molecular, organic, pattern, physiochemical, post-translational, primary, protein, protein sequence motifs and active sites databases, residue, rna, site, spatial, specificity, structural, structure, tertiary |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is used by: PASSer has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
PMID:15608173 | nif-0000-21317 | SCR_008227 | 2026-08-08 12:04:21 | 1 | ||||||||
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Metalloprotein Ligand Interaction Database Resource Report Resource Website |
Metalloprotein Ligand Interaction Database (RRID:SCR_008996) | MetLigDB | database, data or information resource | A publicly accessible web-based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail. Additional information can also be retrieved including protein and inhibitor names, the amino acid residues coordinated to the central metal ion, and the binding affinity of the inhibitor for the target metalloprotein. | metalloprotein, crystallography, protein structure, pdb | is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) | Free | nlx_152607 | SCR_008996 | MetLigDB | 2026-08-08 12:04:25 | 0 |
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