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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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LIGand Attachment SITE Database Resource Report Resource Website 1+ mentions |
LIGand Attachment SITE Database (RRID:SCR_013172) | data or information resource, database | A gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex. Both a redundant and a non-redundant (sequence identity lower than 25) version is available. Quaternary structures proposed by PQS (2) are used for all structures in the dataset. The availability of both unbound and bound structures for each protein guarantees that our dataset can be used to benchmark binding site prediction methods, in conditions that mimic cases where the binding site is truly unknown. In cases where several different bound structures are available for a given protein, all are used to define the binding sites. |
has parent organization: University of Toronto; Ontario; Canada has parent organization: King's College London; London; United Kingdom |
nif-0000-03083 | SCR_013172 | LigASite | 2026-09-02 05:44:37 | 2 | ||||||||||
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DBAli. A Database of Structure Alignments. Resource Report Resource Website |
DBAli. A Database of Structure Alignments. (RRID:SCR_013418) | data or information resource, database | DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali. | protein, protein structure comparison | nif-0000-02725 | SCR_013418 | DBAli | 2026-09-02 05:44:51 | 0 | ||||||||||
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DomIns: A Web Resource for Domain Insertions in Known Protein Structures Resource Report Resource Website 1+ mentions |
DomIns: A Web Resource for Domain Insertions in Known Protein Structures (RRID:SCR_013417) | data or information resource, database | DomIns is a web resource aimed at providing comprehensive information on domain insertions in proteins of known structure. We have followed the definition of protein domains as in the SCOP (Structural Classification of Proteins) database in order to identify insertions. We have considered only the major five classes (All-alpha, All-beta, alpha/beta, alpha+beta and Small Proteins), the fold and the superfamily level of SCOP hierarchy for identifying insertions. Apart from browsing insertions in whole PDB, we also provide an option to browse insertions in a pre-computed list of non-redundant PDB chains provided by PDB_Select with a sequence identity threshold of 90%. | domain insertion of protein, protein domain, protein structure | nif-0000-02760 | SCR_013417 | DomIns | 2026-09-02 05:44:36 | 1 | ||||||||||
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KNOTTIN database Resource Report Resource Website 10+ mentions |
KNOTTIN database (RRID:SCR_013263) | KNOTTIN Database | data or information resource, database | The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the Inhibitor Cystine Knot (ICK) motif/family/fold). Knottins are intriguing miniproteins with strong potential in drug design. This knot is achieved when one disulfide bridge crosses the macrocycle formed by the two other disulfides and the interconnecting backbone. | nif-0000-03074 | SCR_013263 | 2026-09-02 05:44:41 | 12 | |||||||||||
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H-InvDB Resource Report Resource Website 10+ mentions |
H-InvDB (RRID:SCR_013265) | H-InvDB, H-InvDB cDNA, H-InvDB locus | data or information resource, database | H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs. | human gene, human genome, transcripts, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Institute of Advanced Industrial Science and Technology |
nif-0000-02936, biotools:h-invdb | https://bio.tools/h-invdb | SCR_013265 | H-Invitational Database, H-InvDB cDNA, H-InvDB locus, H-InvDB: Annotated Human Gene Database | 2026-09-02 05:44:35 | 25 | |||||||
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ExTopoDB Resource Report Resource Website 1+ mentions |
ExTopoDB (RRID:SCR_013143) | ExTopoDB | data or information resource, database | A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction). | transmembrane protein, protein structure, topological model, blast, transmembrane, protein, model |
is listed by: 3DVC has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20601677 | Public | nlx_151724 | SCR_013143 | 2026-09-02 05:44:40 | 2 | |||||||
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Chloroplast Genome Database Resource Report Resource Website 10+ mentions |
Chloroplast Genome Database (RRID:SCR_013421) | data or information resource, database | The Chloroplast Genome Database contains annotated chloroplast/plastid genomes from the NCBI Organelle Genomes section at NCBI. Users can search for genes by their annotated names, conduct flexible BLAST searches, download protein and nucleotide sequences extracted from a selected chloroplast genome, and browse the putative protein families (tribes) created using TribeMCL. | chloroplast, chloroplast genome, nucleotide sequence, plastid genome, protein sequence, software |
is listed by: 3DVC has parent organization: Pennsylvania State University |
nif-0000-02660 | SCR_013421 | Chloroplast Genome Database | 2026-09-02 05:44:42 | 13 | |||||||||
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CutDB Resource Report Resource Website 10+ mentions |
CutDB (RRID:SCR_013420) | data or information resource, database | The CutDB focuses on the annotation of individual proteolytic events, both actual and predicted. Its offers searchable lists of proteases, Merops code, substrate, and diseases from which users can specify their desired queries in order to obtain more specific information. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content. | predicted proteolytic event, protease, proteolysi | nif-0000-02706 | SCR_013420 | CutDB | 2026-09-02 05:44:36 | 13 | ||||||||||
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MALISAM: Manual ALIgnments of Structurally Analogous Motifs Resource Report Resource Website 1+ mentions |
MALISAM: Manual ALIgnments of Structurally Analogous Motifs (RRID:SCR_013380) | data or information resource, database | MALISAM is a database of pairwise, structure-based alignments for structurally analogous motifs in proteins. Homology and analogy are two alternative scenarios to explain structural similarities among proteins. Homologs inherit similar features from their common ancestor, while analogs converge to similar structures due to a limited number of energetically favorable ways to pack secondary structural elements. Analogous pairs in this database are in three categories: a hybrid motif and a core motif, an interface motif and a core motif, an artificial protein and a natural protein. During evolution, a protein family usually preserves a common core while accumulating insertions and deletions in the periphery. A core motif is composed entirely of secondary structure elements belonging to the evolutionary core. A hybrid motif consists of both core elements and peripheral insertions that are not present in the majority of the family members. An interface motif uses secondary structural elements from two or more domains or subunits contacting along that interface. | nif-0000-03097 | SCR_013380 | MALISAM | 2026-09-02 05:44:42 | 4 | |||||||||||
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Phenylalanine Hydroxylase Locus Knowledgebase Resource Report Resource Website 50+ mentions |
Phenylalanine Hydroxylase Locus Knowledgebase (RRID:SCR_013381) | PAHdb | data or information resource, database | A database of centralized mutation data on the PAH gene. Searchable fields of the database available to users are: mutation name, polymorphic haplotype, population, geographic location, gene region, codon number, mutation type, substitution, phenotype, author's name and many more. The complete information provided for each mutation is regularly updated from both published data and personal communications. | FASEB list | has parent organization: McGill University; Montreal; Canada | nif-0000-03237, r3d100012084 | SCR_013381 | Phenylalanine Hydroxylase Database | 2026-09-02 05:44:36 | 56 | ||||||||
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Human Transcriptome Database for Alternative Splicing Resource Report Resource Website |
Human Transcriptome Database for Alternative Splicing (RRID:SCR_013305) | H-DBAS | data or information resource, database | A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only) | alternative splicing, alternative splicing variant, cdna, transcriptome, h-invitational, rna-seq, rna, comparative genomics |
is listed by: OMICtools has parent organization: National Institute of Advanced Industrial Science and Technology |
PMID:19969536 PMID:17130147 |
nif-0000-02935, OMICS_01887 | SCR_013305 | H-DBAS - Human-transcriptome DataBase for Alternative Splicing | 2026-09-02 05:44:35 | 0 | |||||||
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TCMGeneDIT Resource Report Resource Website 10+ mentions |
TCMGeneDIT (RRID:SCR_013396) | data or information resource, database | TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations. | drug, gene, antagonistic, biomedical, clinical, disease, ingredient, interaction, life science, literature, medicine, pathway, prescription, protein, regulation, research, synergistic, therapeutic | has parent organization: National Taiwan University; Taipei; Taiwan | National Science Council Taiwan ; NTU Frontier and Innovative Research Projects NTUPFIR-96R0107 |
PMID:18854039 | nif-0000-32868 | SCR_013396 | 2026-09-02 05:44:42 | 14 | ||||||||
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Zebrafish Genome Project Resource Report Resource Website 50+ mentions |
Zebrafish Genome Project (RRID:SCR_013157) | data or information resource, database | Database of zebrafish genome. | Zebrafish, genome |
is related to: Genome Reference Consortium is related to: Zebrafish Information Network (ZFIN) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Freely available | SCR_017503, nif-0000-31931 | https://www.sanger.ac.uk/science/data/zebrafish-genome-project | SCR_013157 | Danio rerio Sequencing Project | 2026-09-02 05:44:49 | 67 | |||||||
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Francisella tularensis Genome Research Resource Report Resource Website 1+ mentions |
Francisella tularensis Genome Research (RRID:SCR_013313) | data or information resource, database | Francisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. rancisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. Please visit the following sections of the website for more details about the tools currently available and those to be available in the near future. News 04/17/2008 F. novicida transposon mutant orders are now being handled by BEI Resources. 03/25/2008 New features have been added to the PSAT synteny analysis tool including a printer friendly version of the genomic neighborhood graphic, a text output of homologs in a region in spreadsheet format, and an option for displaying multiple alignments for a gene against a single comparison genome. 02/07/2008 Proteomics experimental data for F. novicida are now integrated into our genome browser. 02/05/2008 Updated genome annotations can now be submitted using the Panda tool. Your participation is encouraged. Please see the Panda page for more information. 02/04/2008 F. holarctica FTA is now available from Genbank (NC_009749) and has been added to our genome browser Tools Name Description Get surrounding sequence Given a gene, other genome feature, or genome coordinate, displays in FASTA format the surrounding sequence a specified number of nucleotides upstream and downstream Synteny Tool Analyze potential regions of local synteny between the Francisella genomes and any other published bacterial genome | has parent organization: University of Washington; Seattle; USA | nif-0000-30585 | SCR_013313 | Francisella tularensis | 2026-09-02 05:44:37 | 2 | ||||||||||
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Elephant shark genome sequencing Resource Report Resource Website 50+ mentions |
Elephant shark genome sequencing (RRID:SCR_013158) | data or information resource, database, service resource | To explore the elephant shark genome, we have conducted a survey-sequencing and comparative analysis of the elephant shark genome in collaboration with J. Craig Venter Institute. The elephant shark sequences generated under this project have been deposited at GenBank under the project accession number AAVX01000000. The sequences can also be searched using BLAST and retrieved here. Cartilaginous fishes (Chondrichthyes) represented by sharks, rays, skates and chimaeras, are phylogenetically the oldest group of living jawed vertebrates. They constitute an important group for our understanding of the origins of the complex developmental and physiological systems of jawed vertebrates. They are also an useful outgroup for bony vertebrates such as tetrapods and teleost fishes and help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. The elephant shark (Callorhinchus milii), also known as the elephant fish and ghost shark, is a chimaera belonging to the Order Chimaeriformes and Family Callorhynchidae. It has the smallest genome among the known cartilaginous fish genomes. Thus, it was proposed as a model cartilaginous fish genome for whole-genome sequencing and comparative analysis (Venkatesh et al. 2005. Curr. Biol. 15: R82-R83). The following resources of the elephant shark are available for the scientific community: *Elephant Shark 1.4x assembly fasta sequences zipped 227 megabytes *Genomic DNA *~8x coverage BAC library (average insert size, ~150 kb) *cDNA libraries (under construction) *cDNA (dated 11 April 2008) with orthologs in 5 vertebrates (human, opossum, chicken, frog, fugu) | FASEB list | has parent organization: Institute of Molecular and Cell Biology; Singapore; Singapore | Agency for Science Technology and Research | PMID:9254694 PMID:17185593 PMID:17407382 |
nif-0000-30511 | SCR_013158 | 2026-09-02 05:44:34 | 84 | ||||||||
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MIMIC II Resource Report Resource Website 10+ mentions |
MIMIC II (RRID:SCR_013237) | data or information resource, database | MIMIC II (Multiparameter Intelligent Monitoring in Intensive Care) Database contains comprehensive clinical data from tens of thousands of Intensive Care Unit (ICU) patients. Data were collected between 2001 and 2008 from a variety of ICUs (medical, surgical, coronary care, and neonatal) in a single tertiary teaching hospital. The database contains clinical data from bedside workstations as well as hospital archives. The database also includes thousands of records of continuous high-resolution physiologic waveforms and minute-by-minute numeric time series (trends) of physiologic measurements. | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nlx_15477 | SCR_013237 | MIMIC, Multiparameter Intelligent Monitoring in Intensive Care | 2026-09-02 05:44:35 | 11 | ||||||||||
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EPGD Resource Report Resource Website 1+ mentions |
EPGD (RRID:SCR_013364) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. EPGD isfocused on the paralogs and the duplication events in the evolution. It is gene-centered and organized by paralog family. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website in plain text files. The database will be very useful for both experimentalists and bioinformaticians for the study of duplication events or paralog families. | evolution, evolution duplication events, paralog | has parent organization: Chinese Academy of Sciences; Beijing; China | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02807 | SCR_013364 | EPGD | 2026-09-02 05:44:38 | 1 | ||||||||
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JAIL- Just Another Interface Library Resource Report Resource Website |
JAIL- Just Another Interface Library (RRID:SCR_013366) | data or information resource, database | JAIL is a database that classifies the interfaces between domain architectures and those between protein chains and between proteins and nucleic acids. Interacting proteins are difficult to crystallize and rarely present within the Protein Data Base. Nevertheless, it is essential to analyze the interacting parts of the proteins to understand the process of protein-protein docking. To overcome this problem we have built up the JAIL database. Since interacting domains exhibit similar structural features than proteins, all known interfaces between interacting domains of the SCOP database were extracted and classified in JAIL. Only a part of all protein structures are included in SCOP. Particularly, new PDB entries are not yet annotated. To overcome this problem additionally all interfaces between protein chains were calculated and included in the database. This type of interface also comprises the interacting parts of the assumed biological units. The last important type of interfaces provided here is composed of the interacting parts between proteins and nucleic acids. Overall the data set consists of about 180,000 interfaces. JAIL is a comfortable tool to browse through the interface library and to analyze single interfaces. However, more general questions require large-scale analysis. For this purpose, a detailed form enables the compiling of comprehensive non redundant data sets for download. | has parent organization: University Medicine Berlin; Berlin; Germany | nif-0000-03060 | SCR_013366 | JAIL | 2026-09-02 05:44:36 | 0 | ||||||||||
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Tree families database Resource Report Resource Website 50+ mentions |
Tree families database (RRID:SCR_013401) | data or information resource, database | A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics | evolutionary history, gene, gene families, genome, animal, comparative genomics, historical duplications, human, invertebrate, losses, ortholog, outgroup genes like yeast (s. cerevisiae and s. pombe), paralog, phylogenetic tree, plant (a. thaliana), single-metazoan animals, speciations, vertebrate, FASEB list |
is related to: FlyMine has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
nif-0000-03588 | SCR_013401 | Tree families database, TreeFam | 2026-09-02 05:44:38 | 88 | |||||||||
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Greglist Resource Report Resource Website 1+ mentions |
Greglist (RRID:SCR_013407) | data or information resource, database | A database listing potential G-quadruplex regulated genes. G-rich DNA sequences can form G-quadruplexes, a four-stranded structure that is stabilized by planar arrays of four guanines associated with hydrogen bonds. Promoter G-quadruplexes have emerged as a new way to regulate gene transcription, such as in c-MYC expression. Further, G-quadruplex motifs are highly enriched in gene promoter regions in humans and other mammals. Greglist contains genes whose promoter regions have G-quadruplex motifs, and these genes are highly likely to be regulated by G-quadruplexes. | g-quadruplex, promoter g-quadruplexes, gene |
is listed by: 3DVC has parent organization: Tianjin University; Tianjin; China |
nif-0000-02929 | SCR_013407 | Greglist | 2026-09-02 05:44:51 | 4 |
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