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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	data or information resource, data repository, database, service resource, storage service resource	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		DOE ; NIH ; 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	SciCrunch Registry	RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank	2026-09-26 02:15:08	12459
Rutgers University; New Jersey; USA Resource Report Resource Website 10+ mentions	Rutgers University; New Jersey; USA (RRID:SCR_011508)		university	Rutgers, The State University of New Jersey, commonly referred to as Rutgers University, Rutgers, or RU, is public research university in New Jersey.		is affiliated with: Big Ten Cancer Research Consortium is parent organization of: CSDeconv is parent organization of: RESBIO is parent organization of: Nucleic Acid Database is parent organization of: Gene Expression Profiling in Spinal Cord Injury is parent organization of: SLIQ is parent organization of: SOPRA is parent organization of: RUcore is parent organization of: Ligand Expo is parent organization of: NIMH Repository and Genomics Resources is parent organization of: BPS- Database of RNA Base-pair Structures is parent organization of: TargetDB: Structural Genomics Target Search is parent organization of: Buzsaki Lab is parent organization of: Human Cancer Protein Interaction Network is parent organization of: MAP-O-MAT is parent organization of: Rutgers Cell and DNA Repository is parent organization of: Rutgers University Labs and Facilities is parent organization of: Rutgers University Waksman Institute of Microbiology Genomics Core Facility is parent organization of: Rutgers New Jersey Medical School; New Jersey; USA is parent organization of: Rutgers Waksman Institute of Microbiology Labs and Facilities is parent organization of: EMDataResource.org is parent organization of: TreQ is parent organization of: BSD - Biodegradative Strain Database is parent organization of: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is parent organization of: National Institute on Drug Abuse Center for Genetic Studies is parent organization of: PDB-Dev is parent organization of: Tunable Biclustering Algorithm is parent organization of: Rutgers University New Jersey Medical School Cellular Imaging and Histology Core Facility					nlx_14806, ISNI:0000 0004 1936 8796, grid.430387.b, Crossref funder ID:100007558, Wikidata:Q499451	https://ror.org/05vt9qd57		SCR_011508	SciCrunch Registry		2026-09-26 02:14:54	15
University of California at San Diego; California; USA Resource Report Resource Website 10+ mentions	University of California at San Diego; California; USA (RRID:SCR_011625)	UCSD	university	The University of California, San Diego, also known as UC San Diego, is public research university located in the La Jolla neighborhood of San Diego, California, in the United States. Established in 1960, UCSD has 6 different campuses.	undergraduate, graduate, master's, doctoral, phD, institution, university	is listed by: DataCite is affiliated with: Diabetes Research Centers is affiliated with: mysamplesize is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: Collaboratory of AIDS Researchers for Eradciation (CARE) is related to: redcap-to-nda is related to: auto-scoring is related to: FIONASITE is related to: Minimally-Processed-Image-Sharing is related to: timeline-followback is related to: little-man-task is related to: redcap-completion is related to: eprime-data-clean is related to: Fast-Track-Image-Sharing is related to: simple-t1-motion-detection is related to: tick-tock is related to: FIONA-QC-PHANTOM is related to: numerical-fitting is related to: aux-file-upload is related to: FIONA-protocol-compliance is related to: redcap-hook-framework is related to: nih-ipad-app-end-point is related to: ABCDreport is related to: delay-discounting is related to: redcap-importer is related to: pearson-central-end-point is related to: abcd-dev is related to: LungMap is related to: Lung Genome Browser is related to: Common Metabolic Disease Genome Atlas has parent organization: University of California; California; USA is parent organization of: MPScope is parent organization of: University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities is parent organization of: BindingDB is parent organization of: OntoMorph Tab is parent organization of: Digital Asset Management System is parent organization of: CARTA is parent organization of: MitoProteome is parent organization of: 3DVC is parent organization of: UCSD Center for NMR Spectroscopy and Imaging of Proteins is parent organization of: Kawasaki Disease Dataset is parent organization of: San Diego Supercomputer Center is parent organization of: UCSD Cognitive Science: The Future of Cognitive Science is parent organization of: Shiley-Marcos Alzheimer's Disease Research Center is parent organization of: University of California at San Diego Department of Psychiatry is parent organization of: Swartz Center for Computational Neuroscience is parent organization of: Cell Centered Database is parent organization of: National Center for Microscopy and Imaging Research is parent organization of: National Biomedical Computation Resource is parent organization of: Center for Research in Biological Systems is parent organization of: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis is parent organization of: La Jolla Interdisciplinary Neurosciences Center is parent organization of: Neuroscience Information Framework is parent organization of: Brainscape is parent organization of: SciCrunch is parent organization of: MAGI is parent organization of: iDASH is parent organization of: UCSD-TV is parent organization of: Network Data Exchange (NDEx) is parent organization of: bioCADDIE is parent organization of: UC San Diego Biorepository is parent organization of: National Resource for Network Biology is parent organization of: Lifesharing Tissue Services is parent organization of: Velvet-SC is parent organization of: Transporter Classification Database is parent organization of: Arnaud Delormes Programs Overview is parent organization of: IntegromeDB is parent organization of: SciVee is parent organization of: EEG / ERP Data Set is parent organization of: UCSD Experimental Neuropath Laboratory is parent organization of: FORCE11 is parent organization of: HIV Neurobehavioral Research Center is parent organization of: cd-hit-454 is parent organization of: OneLab is parent organization of: Systems Transcriptional Activity Reconstruction is parent organization of: HeadIT is parent organization of: BiGG Database is parent organization of: Research Accelerator is parent organization of: Rosalind is parent organization of: Divvy is parent organization of: AbsCN-seq is parent organization of: LIPID Metabolites And Pathways Strategy is parent organization of: UCSD-Nature Signaling Gateway Molecule Pages is parent organization of: Whole Brain Catalog is parent organization of: CCHDO is parent organization of: CD-HIT is parent organization of: SDSC Biology Workbench is parent organization of: Swami: The Next Generation Biology Workbench is parent organization of: Booly: A Resource for Biological Data Integration is parent organization of: Molecule pages in neurobiology is parent organization of: University of California, San Diego, Department of Pharmacology is parent organization of: Combinatorial Extension (CE) is parent organization of: Homophila is parent organization of: University of California San Diego Department of Neurosciences is parent organization of: Archives of General Psychiatry is parent organization of: Cal-IT2: Immersive Visualization Laboratory is parent organization of: Institute for Neural Computation is parent organization of: CHARTER - CNS HIV Antiretroviral Therapy Effects Research is parent organization of: Multimodal Imaging Laboratory is parent organization of: Center for Computational Mass Spectrometry is parent organization of: Joint Center for Structural Genomics is parent organization of: Alzheimer's Disease Cooperative Study is parent organization of: Ion Simulator Interface is parent organization of: BioLit is parent organization of: Conical: The Computational Neuroscience Class Library is parent organization of: Digital Fish Library is parent organization of: UCSD Center for AIDS Research Molecular Biology Core is parent organization of: Grid Enabled Molecular Science Through Online Networked Environments is parent organization of: Finite Element Toolkit is parent organization of: Disease Phenotype Ontology is parent organization of: PTSD-TBI INTRuST is parent organization of: Kawasaki Disease Dataset2 is parent organization of: Pediatric Imaging Neurocognition and Genetics is parent organization of: Cerebral Blood Flow Database and Analysis Pipeline is parent organization of: CBFBIRN is parent organization of: UCSD Digital Collections is parent organization of: SIGnAL Salk Institute Genomic Analysis Laboratory is parent organization of: Datamonkey is parent organization of: EULER-SR is parent organization of: Omics Discovery Index is parent organization of: Dangerous Ideas is parent organization of: University of California San Diego School of Medicine; California; USA is parent organization of: ICA (Independent Component Analysis) for dummies is parent organization of: SpikeNET is parent organization of: HOMER is parent organization of: Hammer is parent organization of: CAMERA is parent organization of: RAMMCAP is parent organization of: WebMGA is parent organization of: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is parent organization of: Alliance for Cellular Signaling Molecule Pages Database is parent organization of: Unys is parent organization of: Mass spectrometry Interactive Virtual Environment (MassIVE) is parent organization of: UCSD Human Milk Biorepository is parent organization of: Reprever is parent organization of: NIDDK Information Network (dkNET) is parent organization of: Cytoscape is parent organization of: BrainInfo is parent organization of: Kepler is parent organization of: TOPSAN is parent organization of: Virmid is parent organization of: neurospy is parent organization of: LAMHDI: The Initiative to Link Animal Models to Human DIsease is parent organization of: HED Tags is parent organization of: Molecular Dynamics Workflow (BioKepler) is parent organization of: Drug Design Data Resource is parent organization of: RepeatScout is parent organization of: GenomeSpace is parent organization of: geocoding is parent organization of: enroll is parent organization of: findMotif.pl is parent organization of: Diabetes Epigenome Atlas is parent organization of: Diabetes Epigenome Atlas is parent organization of: Lab Streaming Layer is parent organization of: Brainome portal is parent organization of: SPARC Anatomy Working Group is parent organization of: Open Science Chain is parent organization of: GNPS is parent organization of: COVID-19 Data Discovery from Clinical Records is parent organization of: FAIR Data Informatics Laboratory is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: Cocaine Biobank is parent organization of: C-GORD is parent organization of: University of California at San Diego Electron Microscopy Core Facility is parent organization of: University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy is parent organization of: Flye is parent organization of: Open Data Commons for Spinal Cord Injury is parent organization of: MetGENE is parent organization of: ReDU is parent organization of: Cell Image Library (CIL) is parent organization of: Open Data Commons for Traumatic Brain Injury has organization facet: Taiji					Crossref Funder ID 100007911, ISNI 0000 0001 2107 4242, Wikidata Q622664, nlx_71933, GRID grid.266100.3, SCR_016626	https://api.datacite.org/dois?prefix=10.6075, https://ror.org/0168r3w48		SCR_011625	SciCrunch Registry	University of California San Diego, University of California San Diego; California; USA, UC San Diego, UC San Diego; California; USA	2026-09-26 02:14:56	11
Structural Genomics Consortium Resource Report Resource Website 50+ mentions	Structural Genomics Consortium (RRID:SCR_003890)	SGC	consortium, data or information resource, organization portal, portal	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.	basic science, drug discovery, drug, structural genomics, genomics, 3d structure, protein, human parasite, drug target, structure, human protein, protocol, phylogenetic tree, histone tail, high-throughput protein crystallization, lex bubbling system, reagent, epigenetic probe, antibody, vector, plasmid, construct	uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Addgene uses: GenBank is related to: AbbVie is related to: Canada Foundation for Innovation is related to: Canadian Institutes of Health Research is related to: Genome Canada is related to: Janssen Research and Development is related to: Ontario Ministry of Economic Development Employment and Infrastructure is related to: Pfizer Animal Genetics is related to: Wellcome Trust has parent organization: University of Oxford; Oxford; United Kingdom has parent organization: University of Toronto; Ontario; Canada	Cancer, Diabetes, Obesity, Psychiatric disorder, Altzheimer	AbbVie ; Boehringer Ingelheim ; Canada Foundation for Innovation ; Canadian Institutes of Health Research ; Genome Canada ; GlaxoSmithKline ; Janssen ; Lilly Canada ; Novartis Research Foundation ; Ontario Ministry of Economic Development Employment and Infrastructure ; Pfizer ; Takeda ; Wellcome Trust		Restricted	nlx_158220			SCR_003890	SciCrunch Registry	Structural Genomics Consortium	2026-09-26 02:13:34	65
InterEvol database Resource Report Resource Website 10+ mentions	InterEvol database (RRID:SCR_006054)	InterEvol	analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource	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	structure, evolution, protein complex, interface, protein complex, sequence alignment, plug in, protein structure, visualization, pymol plugin, structural homolog, structural interolog, bio.tools	is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: CEA; Gif sur Yvette; France		Commissariat a lEnergie Atomique ; ANR HPGenVar	PMID:22053089	Free and open to all users - no login requirement	nlx_151453, biotools:interevol	https://bio.tools/interevol		SCR_006054	SciCrunch Registry		2026-09-26 02:13:59	10
Polbase Resource Report Resource Website	Polbase (RRID:SCR_006107)		data or information resource, data repository, database, service resource, storage service resource	Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.	dna polymerase repository, 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: PubMed is related to: UniProt has parent organization: New England Biolabs		Small Business Innovation Research ; NIGMS 1R44GM087021	PMID:21993301	Free, Open unspecified license, Acknowledgement required	biotools:polbase, nlx_151580	https://bio.tools/polbase		SCR_006107	SciCrunch Registry	DNA Polymerase Database	2026-09-26 02:14:00	0
NMR Restraints Grid Resource Report Resource Website	NMR Restraints Grid (RRID:SCR_006127)	NMR Restraints Grid	data or information resource, database, 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	SciCrunch Registry	BMRB NMR Restraints Grid	2026-09-26 02:14:00	0
PDBsum Resource Report Resource Website 500+ mentions	PDBsum (RRID:SCR_006511)	PDBsum	analysis service resource, d spatial image, data analysis service, data or information resource, database, production service resource, service resource	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.	3d structure, protein, molecule, structure, protein chain, dna, ligand, metal ion, interaction, gold standard	is related to: ProFunc is related to: SAS - Sequence Annotated by Structure is related to: ArchSchema is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DrugPort is related to: Enzyme Structures Database has parent organization: European Bioinformatics Institute		Wellcome Trust	PMID:18996896 PMID:15608193 PMID:11125097 PMID:9433130		nlx_40623			SCR_006511	SciCrunch Registry		2026-09-26 02:14:05	634
Enzyme Structures Database Resource Report Resource Website 1+ mentions	Enzyme Structures Database (RRID:SCR_007125)	EC->PDB, EC-PDB	data or information resource, database, 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	SciCrunch Registry		2026-09-26 02:14:14	3
GlyVicinity Resource Report Resource Website 1+ mentions	GlyVicinity (RRID:SCR_001567)	GlyVicinity	analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource	Service to generate statistics about the amino acids present in the vicinity of carbohydrate residues. Besides the amino acids in sequential neighborhood of glycosylation sites (analysed by GlySeq), those in the spatial vicinity of carbohydrate residues determine the characteristics of glycoproteins. The latter ones are of special interest for the examination of carbohydrate-binding proteins. Since carbohydrate moieties are not covalently bound in these cases, sequence analysis comparable to that for glycosylation sites is not possible there. GlyVicinity performs statistical analyses on the types of amino acids around carbohydrate chains and on the atoms forming the closest contacts between protein and carbohydrate residues. Results are based on weekly updated datasets derived from the Protein Data Bank (PDB).	carbohydrate, amino acid, carbohydrate residue, statistical analysis	is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: glycosciences.de		DFG	PMID:15608187	THIS RESOURCE IS NO LONGER IN SERVICE	nlx_152880			SCR_001567	SciCrunch Registry	GlyVicinity: Analysis of Amino Acids in the Vicinity of Carbohydrate Residues contained in the Protein Data Bank (PDB)	2026-09-26 02:13:01	1
NIDDK Information Network (dkNET) Resource Report Resource Website 10+ mentions	NIDDK Information Network (dkNET) (RRID:SCR_001606)	dkNET	community building portal, data or information resource, database, portal	The NIDDK Information Network (dkNET) is a community-based network to serve needs of basic and clinical investigators that includes large pools of data and research resources relevant to mission of National Institute of Diabetes and Digestive and Kidney Disease.	dknet, data resource, diabetes, kidney, liver, disease, urology, hematology, digestive, nutrition, endocrine, obesity, metabolic	uses: NIDDK Central Repository uses: Addgene uses: NIF Data Federation uses: Antibody Registry uses: Nuclear Receptor Signaling Atlas uses: GenitoUrinary Development Molecular Anatomy Project uses: Diabetic Complications Consortium uses: National Mouse Metabolic Phenotyping Centers uses: T1DBase uses: Beta Cell Biology Consortium uses: Grants.gov uses: dkNET Community Pilot Funding Opportunities uses: Integrated Grants uses: ClinicalTrials.gov uses: Integrated Animals uses: Intestinal Stem Cell Consortium recommends: Biological General Repository for Interaction Datasets (BioGRID) recommends: Cell Image Library (CIL) recommends: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) recommends: NIDDK Central Repository recommends: Network Data Exchange (NDEx) recommends: PeptideAtlas recommends: International Mouse Phenotyping Consortium (IMPC) recommends: FlyBase recommends: Metabolomics Workbench recommends: Zebrafish Information Network (ZFIN) recommends: Mouse Genome Informatics (MGI) recommends: Database of Interacting Proteins (DIP) recommends: UniProt recommends: PhysioNet recommends: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) recommends: ClinicalTrials.gov recommends: dbVar recommends: Analysis, Visualization, and Informatics Lab-space (AnVIL) recommends: WormBase recommends: dbSNP recommends: GenBank recommends: DNA DataBank of Japan (DDBJ) recommends: Database of Genomic Variants Archive (DGVa) recommends: NCBI Sequence Read Archive (SRA) recommends: MGnify recommends: European Variation Archive (EVA) recommends: European Nucleotide Archive (ENA) recommends: Gene Expression Omnibus (GEO) recommends: NCBI Assembly Archive Viewer recommends: Protein Circular Dichroism Data Bank (PCDDB) recommends: miRBase recommends: Trace Archive recommends: UniProtKB recommends: Coherent X-Ray Imaging Data Bank (CXIDB) recommends: Electron Microscopy Data Bank at PDBe (MSD-EBI) recommends: Worldwide Protein Data Bank (wwPDB) recommends: Biological Magnetic Resonance Data Bank (BMRB) recommends: Crystallography Open Database (COD) recommends: PDBj - Protein Data Bank Japan recommends: Inorganic Crystal Structure Database (ICSD) recommends: Structural Biology Grid recommends: NCBI database of Genotypes and Phenotypes (dbGap) recommends: ArrayExpress recommends: EMDataResource.org recommends: Cambridge Crystallographic Data Centre (CCDC) recommends: PDBe - Protein Data Bank in Europe recommends: Japanese Genotype-phenotype Archive (JGA) recommends: PubChem BioAssay recommends: European Genome phenome Archive recommends: GenomeRNAi recommends: ProteomeXchange recommends: MetaboLights recommends: IntAct recommends: FLOWRepository recommends: Proteomics Identifications (PRIDE) recommends: Global Proteome Machine Database (GPM DB) recommends: Kinetic Models of Biological Systems (KiMoSys) recommends: ChEMBL recommends: Cancer Imaging Archive (TCIA) recommends: Image Data Resource (IDR) recommends: The Immunology Database and Analysis Portal (ImmPort) recommends: PubChem Substance recommends: NeuroMorpho.Org recommends: Cancer Nanotechnology Laboratory (caNanoLab) recommends: SICAS Medical Image Repository recommends: Mass spectrometry Interactive Virtual Environment (MassIVE) recommends: Dryad Digital Repository recommends: ZENODO recommends: NIH Figshare Archive recommends: STRENDA recommends: OpenNeuro recommends: Influenza Research Database (IRD) recommends: 1000 Functional Connectomes Project recommends: Mendeley Data recommends: Open Science Framework recommends: Dataverse Network Project recommends: NIMH Data Archive recommends: FigShare recommends: National Addiction and HIV Data Archive Program (NAHDAP) recommends: SPARC Portal recommends: Vivli is recommended by: National Library of Medicine lists: Diabetic Complications Consortium lists: Nephromine lists: LIPID Metabolites And Pathways Strategy lists: METLIN lists: NIDDK Inflammatory Bowel Disease Genetics Consortium lists: Body Mass Index Calculator lists: Symptom Score for Benign Prostatic Hyperplasia lists: Genetics of Kidneys in Diabetes lists: Type 1 Diabetes - Rapid Access to Intervention Development lists: TEDDY lists: Trans-Institute Angiogenesis Research Program lists: Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease lists: Current Research Information System lists: Healthy People lists: Acute Liver Failure Study Group lists: Collaborative Islet Transplant Registry lists: Diabetes Prevention Type 1 lists: Epidemiology of Diabetes Interventions and Complications lists: NIH Division of Nutrition Research Coordination lists: Human Nutrition Research Information Management lists: Type 1 Diabetes Resource lists: National Diabetes Education Program lists: Pediatric Acute Liver Failure Study lists: Globin Gene Server lists: NIH Chronic Prostatitis Symptom Index lists: Sequencing of Idd regions in the NOD mouse genome lists: Look AHEAD lists: Teen-Longitudinal Assessment of Bariatric Surgery lists: Adult to Adult Living Donor Liver Transplantation Cohort Study lists: Behavior Enhances Drug Reduction of Incontinence lists: BARI 2D lists: Childhood Liver Disease Research and Education Network lists: Standardization of C-peptide measurements lists: CKID A Prospective Cohort Study of Kidney Disease in Children lists: Diabetes Prevention Program lists: Diabetes Prevention Program Outcomes Study lists: Irritable Bowel Syndrome Outcome Study lists: Folic Acid for Vascular Outcome Reduction in Transplantation lists: Type 1 Diabetes TrialNet lists: Diabetes Research in Children Network lists: Diabetic Retinopathy Clinical Research Network lists: Clinical Islet Transplantation Study lists: Nonalcoholic Steatohepatitis Clinical Research Network lists: Drug-Induced Liver Injury Network lists: Family Investigation of Nephropathy of Diabetes lists: Frequent Hemodialysis Network Daily Trial lists: HEALTHY study lists: SISTEr lists: Urinary Incontinence Treatment Network lists: TINSAL-T2D lists: TOMUS lists: Type 1 Diabetes Genetics Consortium lists: Center for Inherited Disease Research lists: Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION) lists: Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) lists: Lifestyle Interventions for Expectant Moms (LIFE-Moms) lists: Hyperglycemia and 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lists: Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Integrated Physiology Core lists: Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Image Core lists: Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Proteomics Core lists: Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Translational Research Enhancement Core lists: UCSF Liver Center lists: UCSF Liver Center Cell Biology Core lists: UCSF Liver Center Clinical & Translational Core lists: UCSF Liver Center Immunology Core lists: UCSF Liver Center Pathology & Imaging Core lists: University of Chicago Digestive Diseases Research Core Center lists: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core lists: University of Chicago Digestive Diseases Research Core Center Administrative Core lists: University of Chicago Digestive Diseases Research Core Center Tissue 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Management Core lists: University of North Carolina Center for Gastrointestinal Biology and Disease Gnotobiotic Core lists: University of North Carolina Center for Gastrointestinal Biology and Disease Histology Core lists: University of North Carolina Center for Gastrointestinal Biology and Disease Large Animal Models Core lists: University of North Carolina Center for Gastrointestinal Biology and Disease Microbiome Core lists: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases lists: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core lists: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Host-Microbial Analytic and Repository Core lists: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Genetically-Modified Mouse Core lists: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core lists: Joslin Diabetes Center Molecular Phenotyping and Genotyping Core lists: University of Pennsylvania Diabetes Research Center lists: Preventing Early Renal Loss in Diabetes (PERL) lists: Clinical Trials in Organ Transplantation in Children (CTOT-C) lists: Clinical Trials in Organ Transplantation (CTOT) lists: Stanford Diabetes Research Center lists: Monogenic Diabetes Registry lists: Chronic Prostatitis Collaborative Research Network Clinical Trial- Alfuzosin lists: National Glycohemoglobin Standardization Program lists: MetaCyto lists: JOINSOLVER lists: HASP lists: NetCirChro lists: Simmune lists: ABC Bacterial Transporter Systems Database lists: Kidney Precision Medicine Project lists: ValIdated Systematic IntegratiON of epigenomic data lists: The Human BioMolecular Atlas Program lists: Prevention of Lower Urinary Tract Symptoms lists: Illuminating the Druggable Genome lists: 4D Nucleome lists: immuneXpresso lists: Multi-Disciplinary Approach to the Study of Chronic Pelvic Pain lists: Secrepedia lists: MoTrPAC Data Hub lists: Human Cell Atlas lists: PANC-DB lists: Rare and Atypical Diabetes Network lists: Diabetes Control and Complications Trial lists: Diabetes Data and Hypothesis Hub lists: Common Metabolic Diseases Knowledge Portal lists: Type 1 Diabetes Knowledge Portal lists: Sleep Disorder Knowledge Portal lists: Cardiovascular Disease Knowledge Portal lists: Cerebrovascular Disease Knowledge Portal lists: Trans-Omics for Precision Medicine (TOPMed) Program lists: All of Us lists: AI-READI is listed by: NIH Data Sharing Repositories is listed by: NIDDK Research Resources is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: MTOPS Prostate Samples Analysis Consortium is related to: Neuroscience Information Framework is related to: Diabetes Disease Portal is related to: Kidney and Urinary Pathway Knowledge Base is related to: dbMHC is related to: Islet Cell Resource Centers is related to: DGAP is related to: Nuclear Receptor Resource is related to: dkCOIN is related to: Human Biological Data Interchange is related to: National Gene Vector Biorepository is related to: Creatinine Standardization Program is related to: Glomerular Filtration Rate Calculators is related to: Congressionally Directed Medical Research Program is related to: National Kidney Disease Education Program is related to: Network of Minority Health Research Investigators is related to: National Endocrine and Metabolic Diseases Information Service is related to: Kidney and Urinary Pathway Ontology is related to: National Diabetes Information Clearinghouse is related to: Digestive Diseases Statistics for the United States is related to: Diabetes in America is related to: National Digestive Diseases Information Clearinghouse is related to: Diabetes Control and Complications Trial is related to: National Hematologic Diseases Information Service is related to: National Kidney and Urologic Diseases Information Clearinghouse is related to: Nonhuman Primate Transplantation Tolerance Cooperative Study Group is related to: Type 1 Diabetes Preclinical Testing Program is related to: Diabetes Autoantibody Standardization Program is related to: AASK Clinical Trial and Cohort Study is related to: Maryland Genetics of Interstitial Cystitis is related to: Frequent Hemodialysis Network Nocturnal Trial is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: Boston Area Community Health Survey is related to: Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia is related to: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study is related to: Complementary and Alternative Medicine for Urological Symptoms is related to: Mouse Mutagenesis Center for Developmental Defects is related to: CARDS Database is related to: ACCORD is related to: Program to Reduce Incontinence by Diet and Exercise is related to: Renal Disease Portal is related to: Renin Angiotensin System Study is related to: NIH Data Sharing Repositories is related to: Kidney Development Database is related to: GenePaint Interactive Anatomy Atlas is related to: EMAGE Gene Expression Database is related to: Gene Expression Omnibus is related to: MGnify is related to: FAIR Data Informatics Laboratory is related to: Type 1 Diabetes Knowledge Portal is related to: Polycystic Kidney Disease Research Resource Consortium has parent organization: SciCrunch has parent organization: University of California at San Diego; California; USA	Digestive disease, Kidney disease, Diabetes, Metabolic disease, Endocrine disease, Obesity, Urologic disease, Type 1 diabetes, Type 2 diabetes	NIDDK U24 DK097771	PMID:26393351	Free, Freely available	nlx_153866, r3d100012845	http://scicrunch.org/dknet, https://doi.org/10.17616/R31NJMEL		SCR_001606	SciCrunch Registry	National Institute of Diabetes and Digestive and Kidney Disease Information Network, NIDDK Information Network, DKnet, NIDDKInformation Network	2026-09-26 02:13:01	21
Community Structure-Activity Resource Resource Report Resource Website 10+ mentions	Community Structure-Activity Resource (RRID:SCR_002206)	CSAR	data or information resource, data repository, data set, service resource, storage service resource	Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.	crystal structure, binding affinity, protein-ligand complex, protein, small molecule, ligand, compound	is used by: NIF Data Federation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Michigan; Ann Arbor; USA		NIGMS		THIS RESOURCE IS NO LONGER IN SERVICE	nlx_154720			SCR_002206	SciCrunch Registry		2026-09-26 02:13:09	16
ConSurf Database Resource Report Resource Website 100+ mentions	ConSurf Database (RRID:SCR_002320)	ConSurfDB	data or information resource, database, 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	SciCrunch Registry	, consurf-db, ConSurf-DataBase, ConSurf-DB, ConSurfDB, ConSurf Server Database, ConSurfDataBase, ConSurf- Data Base	2026-09-26 02:13:11	318
glycosciences.de Resource Report Resource Website 10+ mentions	glycosciences.de (RRID:SCR_002324)	GLYCOSCIENCES.de	data or information resource, database, portal, topical portal	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.	glycoinformatics, glycobiology, glycomics, carbohydrate, 3d structure, data analysis service, modeling, structure, nuclear magnetic resonance, mass spectroscopy, protein, glycan	lists: LiGraph lists: pdb-data lists: PDB2MultiGif is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Giessen; Hesse; Germany is parent organization of: GlyProt is parent organization of: Distance Mapping is parent organization of: pdb-care is parent organization of: pdb2linucs is parent organization of: GlyVicinity is parent organization of: GlyTorsion is parent organization of: GlySeq is parent organization of: LINUCS is parent organization of: sumo is parent organization of: GlycoFragment is parent organization of: Glyco-CD is parent organization of: GlycoMapsDB is parent organization of: SWEET-DB is parent organization of: CARP		DFG	PMID:16239495	Free, Public	nif-0000-21103			SCR_002324	SciCrunch Registry	Glycosciences	2026-09-26 02:13:11	25
PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions	PDBe - Protein Data Bank in Europe (RRID:SCR_004312)	PDBe	data or information resource, data repository, database, service resource, storage service resource	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.	x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools	is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline		European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4	PMID:21045060 PMID:21460450 PMID:19858099		r3d100012791, biotools:pdbe, nlx_32372	https://bio.tools/pdbe, https://doi.org/10.17616/R3J226		SCR_004312	SciCrunch Registry	Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database	2026-09-26 02:13:41	55
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	SciCrunch Registry	U.S. National Library of Medicine	2026-09-26 02:14:53	412
RNA FRABASE - RNA FRAgments search engine and dataBASE Resource Report Resource Website	RNA FRABASE - RNA FRAgments search engine and dataBASE (RRID:SCR_012808)	RNA FRABASE	analysis service resource, d spatial image, data analysis service, data or information resource, database, production service resource, service resource	Engine and 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. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided.	structural element, secondary structure, rna, rna structure, 3d rna fragment, 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: Polish Academy of Sciences Poznan; Poznan; Poland		Foundation for Polish Science SP 01/04; Ministry of Education and Science 3T09A014 29; Polish Ministry of Science and Higher Education PBZ-MniSW-07/1/2007/01; Polish Ministry of Science and Higher Education NN 519314635	PMID:20459631 PMID:17921499		nif-0000-03413, biotools:rna_frabase	https://bio.tools/rna_frabase		SCR_012808	SciCrunch Registry	RNA FRAgments search engine dataBASE, RNA FRAgments search engine and dataBASE, RNA FRABASE - RNA FRAgments search engine dataBASE	2026-09-26 02:17:11	0
PDB2MultiGif Resource Report Resource Website	PDB2MultiGif (RRID:SCR_001489)		software resource, web application	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	SciCrunch Registry	PDB to MultiGIF	2026-09-26 02:17:25	0
HOLLOW Resource Report Resource Website 10+ mentions	HOLLOW (RRID:SCR_005729)	HOLLOW	data processing software, data visualization software, software application, software resource	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	SciCrunch Registry	HOLLOW - Volume Filling of Protein Structures, HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures	2026-09-26 02:17:26	37
pdb2linucs Resource Report Resource Website 1+ mentions	pdb2linucs (RRID:SCR_001566)	pdb2linucs	analysis service resource, data analysis service, production service resource, service resource	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.	carbohydrate, linucs, iupac, structure	is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: LINUCS is related to: GlyTorsion is related to: GlySeq is related to: CARP has parent organization: glycosciences.de		DFG	PMID:15010309	THIS RESOURCE IS NO LONGER IN SERVICE	nlx_152879		http://www.dkfz-heidelberg.de/spec/pdb2linucs/	SCR_001566	SciCrunch Registry		2026-09-26 02:18:10	1

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