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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SuperTarget Resource Report Resource Website 10+ mentions |
SuperTarget (RRID:SCR_002696) | SuperTarget | data or information resource, database | Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. | drug metabolism, drug, cytochrome p450, ontology, pathway, target, compound, cytochrome, drug target, protein, side effect, protein-protein interaction |
is listed by: OMICtools has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
BMBF MedSys 0315450A; DFG RTG Computational Systems Biology GRK1772; DFG IRTG Systems Biology of Molecular Networks GRK1360; European Union SynSys ; NIGMS GM070064 |
PMID:22067455 PMID:17942422 |
Free, Freely available | r3d100012195, nif-0000-00416, OMICS_01591 | http://bioinf-tomcat.charite.de/supertarget/, http://bioinformatics.charite.de/supertarget, https://doi.org/10.17616/R3TM0F | SCR_002696 | 2026-09-19 12:56:37 | 29 | |||||
|
Binding MOAD Resource Report Resource Website 10+ mentions |
Binding MOAD (RRID:SCR_002294) | Binding MOAD | data or information resource, database | Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. | drug, enzymatic, affinity, binding, binding-affinity, biological, chemical, cheminformatic, crystal, crystallography, intermolecular interaction, signaling pathway, ligand, protein, ligand-protein binding, protein crystal structure, protein-ligand, protein-ligand complex |
is used by: Drug Design Data Resource is listed by: OMICtools is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Michigan; Ann Arbor; USA |
MCB 546073 | PMID:18055497 PMID:16168689 PMID:15971202 |
Free, Public, Acknowledgement requested | OMICS_01900, nif-0000-21048 | SCR_002294 | BindingMOAD.org, Binding Mother of All Databases | 2026-09-19 12:56:35 | 18 | |||||
|
EDAS - EST-Derived Alternative Splicing Database Resource Report Resource Website 1+ mentions |
EDAS - EST-Derived Alternative Splicing Database (RRID:SCR_002449) | EDAS | data or information resource, database | Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test. | alternative splicing, gene, protein, mrna, est, exon, intron, rat, dog |
is listed by: OMICtools has parent organization: Moscow State University; Moscow; Russia |
PMID:16909834 | Free, Freely available | nif-0000-02786, OMICS_01885 | SCR_002449 | EDAS: EST Derived Alternative Splicing Database, EST Derived Alternative Splicing Database | 2026-09-19 12:56:36 | 1 | ||||||
|
CASBAH Resource Report Resource Website 1+ mentions |
CASBAH (RRID:SCR_002728) | CASBAH | data or information resource, database | Database which contains information pertaining to all currently known caspase substrates. | protein, caspase substrate, caspase |
is listed by: OMICtools has parent organization: Trinity College Dublin; Dublin; Ireland |
PMID:17273173 | OMICS_03304 | SCR_002728 | The CAspase Substrate dataBAse Homepage, The CASBAH, CAspase Substrate dataBAse Homepage | 2026-09-19 12:56:37 | 4 | |||||||
|
NMR metabolomics database of Linkoping Resource Report Resource Website 1+ mentions |
NMR metabolomics database of Linkoping (RRID:SCR_002758) | MDL | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules. | nuclear magnetic resonance, metabolomics, mac os x, unix/linux, windows |
is listed by: OMICtools has parent organization: Linkoping University; Linkoping; Sweden |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02853 | SCR_002758 | MDL - The Magnetic Resonance Metabolomics Database, Magnetic Resonance Metabolomics Database | 2026-09-19 12:56:37 | 1 | |||||||
|
WoLF PSORT Resource Report Resource Website 100+ mentions |
WoLF PSORT (RRID:SCR_002472) | WoLF PSORT | analysis service resource, data analysis service, production service resource, service resource | Data analysis service for protein subcellular localization prediction. | subcellular localization, protein | is listed by: OMICtools | Restricted | OMICS_01637 | SCR_002472 | WoLF PSORT - Protein Subcellular Localization prediction | 2026-09-19 12:56:36 | 166 | |||||||
|
SECISearch3 and Seblastian Resource Report Resource Website 1+ mentions |
SECISearch3 and Seblastian (RRID:SCR_003186) | SECISearch, Seblastian, SECISearch3 | analysis service resource, data analysis service, production service resource, service resource | Web server to predict eukaryotic selenoproteins and SECIS (SElenoCysteine Insertion Sequences) elements along nucleotide sequences. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. | selenoprotein, nucleotide sequence, selenocysteine insertion sequence, sequence |
is listed by: OMICtools has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:23783574 | Public, Acknowledgement requested | OMICS_01566 | SCR_003186 | Selenoprotein prediction server | 2026-09-19 12:56:39 | 1 | ||||||
|
RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq, https://bio.tools/refseq, https://doi.org/10.17616/R3HP70 | SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-09-19 12:56:40 | 19506 | ||||||
|
Primer-BLAST Resource Report Resource Website 5000+ mentions |
Primer-BLAST (RRID:SCR_003095) | Primer-BLAST | analysis service resource, data analysis service, production service resource, service resource | A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications. | primer, blast, pcr target, polymerase chain reaction, primer design |
is listed by: OMICtools is listed by: SoftCite is related to: Primer3 has parent organization: NCBI |
PMID:22708584 | Free, Freely available | OMICS_02343 | SCR_003095 | 2026-09-19 12:56:38 | 6113 | |||||||
|
PReMod Resource Report Resource Website 10+ mentions |
PReMod (RRID:SCR_003403) | PReMod | data or information resource, database | Database that describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data. | cis-regulatory module, genome, transcription factor binding site, chromosome, module, predict, gene |
is listed by: OMICtools has parent organization: McGill University; Montreal; Canada |
PMID:17148480 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03334, OMICS_01873 | SCR_003403 | Predicted Regulatory Modules | 2026-09-19 12:56:40 | 11 | ||||||
|
MAGI Resource Report Resource Website 10+ mentions |
MAGI (RRID:SCR_003360) | analysis service resource, data analysis service, production service resource, service resource | A web service for fast microRNA-Seq data analysis in a GPU infrastructure. | fastq, c, perl, php, software program, gpu/cuda |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:24907367 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04636 | SCR_003360 | 2026-09-19 12:56:39 | 30 | ||||||||
|
mtDB - Human Mitochondrial Genome Database Resource Report Resource Website 50+ mentions |
mtDB - Human Mitochondrial Genome Database (RRID:SCR_002945) | mtDB | data or information resource, database | A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences. | human genome, mitochondrial dna, sequence, variant, population genetics, coding region, polymorphic site, population, mitochondrial sequence, mitochondrial polymorphism, FASEB list |
is listed by: OMICtools has parent organization: Uppsala University; Uppsala; Sweden |
Swedish Research Council | PMID:16381973 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02994, OMICS_01642 | SCR_002945 | Human Mitochondrial Genome Database | 2026-09-19 12:56:38 | 59 | |||||
|
miRNAMap Resource Report Resource Website 100+ mentions |
miRNAMap (RRID:SCR_003156) | miRNAMap | data or information resource, database | A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA. | microrna, genome, FASEB list |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:18029362 PMID:16381831 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00408, nif-0000-03138 | SCR_003156 | 2026-09-19 12:56:39 | 251 | |||||||
|
ProNIT Resource Report Resource Website 10+ mentions |
ProNIT (RRID:SCR_003431) | ProNIT | data or information resource, database | Database that provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. It contains the properties of the interacting protein and nucleic acid, bibliographic information and several thermodynamic parameters such as the binding constants, changes in free energy, enthalpy and heat capacity. | interaction, protein, nucleic acid, protein-nucleic acid interaction, thermodynamic, binding constant, free energy, enthalpy, heat capacity | is listed by: OMICtools | Japan Society for the Promotion of Science ; Advanced Technology Institute Inc. |
PMID:16381846 PMID:11987161 PMID:11724731 |
Free, Freely available | nif-0000-03347, OMICS_00541 | http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html, http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html | SCR_003431 | 2026-09-19 12:56:40 | 12 | |||||
|
Proteome Analyst Specialized Subcellular Localization Server Resource Report Resource Website 1+ mentions |
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) | PA-SUB | analysis service resource, data analysis service, production service resource, service resource | Web server specialized to predict the subcellular localization of proteins using established machine learning techniques. | subcellular localization, protein, machine learning, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Alberta; Alberta; Canada |
PMID:14990451 | Free, Available for download, Freely available | biotools:pa-sub, OMICS_01631 | https://psort.org/#:~:text=Proteome%20Analyst's%20Subcellular%20Localization%20Server, proteins%20to%20many%20localization%20sites. | SCR_003143 | 2026-09-19 12:56:39 | 1 | ||||||
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PolymiRTS Resource Report Resource Website 100+ mentions |
PolymiRTS (RRID:SCR_003389) | PolymiRTS | data or information resource, database | Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions. | polymorphism, microrna, human, disease, trait, snp, indel, pathway, genetic variant, gene expression, phenotype, chromosome, chromosome location, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PhRMA Foundation ; UT Center for Integrative and Translational Genomics ; NICHD HD052472; NIAAA AA014425; NIDA DA021131; NINR NR009270; NIAID AI081050; NIAID AI019782; American Heart Association 0830134N; United States Department of Defense W81XHW-05-01-0227 |
PMID:24163105 PMID:22080514 |
Free, Available for download, Freely available | nif-0000-03324, biotools:polymirts, OMICS_00391 | https://bio.tools/polymirts | http://compbio.utmem.edu/miRSNP/ | SCR_003389 | Polymorphism in microRNA Target Site, PolymiRTS Database, Polymorphism in microRNAs and their TargetSites | 2026-09-19 12:56:39 | 161 | |||
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FastSNP Resource Report Resource Website 50+ mentions |
FastSNP (RRID:SCR_003140) | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information. | single nucleotide polymorphism, function, phenotype, transcript, prioritize, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Academia Sinica; Taipei; Taiwan |
National Research Program in Genomic Medicine ; National Science Council Taiwan NSC93-3112-B-001-008-Y; National Science Council Taiwan NSC93-3112-B-001-018-Y |
PMID:16845089 | Free, Freely available | biotools:fastsnp, OMICS_00173, nif-0000-30566 | https://bio.tools/fastsnp | http://fastsnp.ibms.sinica.edu.tw/pages/input_CandidateGeneSearch.jsp | SCR_003140 | FastSNP: A Functional Analysis and Selection Tool for SNP in Large Scale Association Study, Function Analysis and Selection Tool for Single Nucleotide Polymorphisms, A Functional Analysis and Selection Tool for SNP in Large Scale Association Study | 2026-09-19 12:56:39 | 62 | ||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | 2026-09-19 12:56:38 | 405 | ||||||
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Chromas Resource Report Resource Website 10+ mentions |
Chromas (RRID:SCR_000598) | Chromas | commercial organization, software resource | Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01016, biotools:chromas | https://bio.tools/chromas | SCR_000598 | 2026-09-19 12:58:30 | 16 | |||||||
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GenVision Resource Report Resource Website 1+ mentions |
GenVision (RRID:SCR_001166) | GenVision | commercial organization, software resource | A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig. | genome, image, visualization, graphic, map, gene expression, contig, genetics |
is listed by: OMICtools works with: Lasergene's SeqMan Pro |
Commercial | OMICS_02135 | SCR_001166 | GenVision - Software for Publication-Quality Illustrations, DNASTAR GenVision | 2026-09-19 12:58:32 | 1 |
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