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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TBLASTN Resource Report Resource Website 5000+ mentions |
TBLASTN (RRID:SCR_011822) | TBLASTN | analysis service resource, data analysis service, production service resource, service resource | Tool to search translated nucleotide databases using a protein query. | protein |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
OMICS_00999 | SCR_011822 | Translated BLAST: tblastn | 2026-09-12 01:02:06 | 5696 | ||||||||
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HSLPred Resource Report Resource Website |
HSLPred (RRID:SCR_011972) | HSLPred | analysis service resource, data analysis service, production service resource, service resource | A support vector machine (SVM)-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins using various features such as i) amino acid composition, ii) dipeptide composition and iii) evolutionary information of proteins. | subcellular localization, protein, support vector machine, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
PMID:15647269 | Acknowledgement requested | biotools:hslpred, OMICS_01622 | https://bio.tools/hslpred | SCR_011972 | HSLPred - A SVM-based Method for Subcellular Localization of Human Proteins | 2026-09-12 01:02:07 | 0 | |||||
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iLoc-Plant Resource Report Resource Website 1+ mentions |
iLoc-Plant (RRID:SCR_011973) | iLoc-Plant | analysis service resource, data analysis service, production service resource, service resource | Data analysis service for predicting subcellular localization of plant proteins with single and multiple sites. | subcellular localization, protein, classifier | is listed by: OMICtools | PMID:21984117 | Acknowledgement requested | OMICS_01624 | SCR_011973 | iLoc-Plant: Predicting subcellular localization of plant proteins with single and multiple sites | 2026-09-12 01:02:07 | 1 | ||||||
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KnowPredsite Resource Report Resource Website 1+ mentions |
KnowPredsite (RRID:SCR_011974) | KnowPredsite | analysis service resource, data analysis service, production service resource, service resource | A knowledge-based data analysis service to predict the localization site(s) of both single-localized and multi-localized proteins. | homolog, protein, subcellular localization |
is listed by: OMICtools has parent organization: Academia Sinica; Taipei; Taiwan |
PMID:19958518 | OMICS_01625 | SCR_011974 | KnowPredsite: A web server for predicting single and multiple subcellular localization sites, KnowPred site, KnowPredsite: A general protein subcellular localization predictor for eukaryotes and prokaryotes | 2026-09-12 01:02:07 | 1 | |||||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-09-12 01:02:09 | 545 | |||||
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BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | analysis service resource, data analysis service, production service resource, service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-09-12 01:02:07 | 46 | ||||||||
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Cell-PLoc Resource Report Resource Website 100+ mentions |
Cell-PLoc (RRID:SCR_011966) | Cell-PLoc | analysis service resource, data analysis service, production service resource, service resource | A package of web-servers for predicting subcellular localization of proteins in different organisms. | subcellular localization, protein, gram-negative protein, gram-positive protein, virus |
is listed by: OMICtools has parent organization: Shanghai Jiao Tong University; Shanghai; China is parent organization of: Euk-mPLoc |
PMID:18274516 | OMICS_01617 | SCR_011966 | Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in different organisms | 2026-09-12 01:02:07 | 254 | |||||||
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CELLO Resource Report Resource Website 1000+ mentions |
CELLO (RRID:SCR_011968) | CELLO | analysis service resource, data analysis service, production service resource, service resource | A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment. | dna, protein, proteomic, genomic |
is used by: Cello2Go is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:15096640 | Acknowledgement requested | OMICS_01618 | SCR_011968 | CELLO: subCELlular LOcalization predictor | 2026-09-12 01:02:07 | 1271 | ||||||
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Antibodypedia Resource Report Resource Website 10+ mentions |
Antibodypedia (RRID:SCR_012782) | data or information resource, database | Open-access database of antibodies against human proteins developed through collaboration between Antibodypedia AB and the Nature Publishing Group. It aims to provide the scientific community and antibody distributors alike with information on the effectiveness of specific antibodies in specific applications--to help scientists select the right antibody for the right application. Antibodypedia's mission is to promote the functional understanding of the human proteome and expedite analysis of potential biomarkers discovered through clinical efforts. To this end, they have developed an open-access, curated, searchable database containing annotated and scored affinity reagents to aid users in selecting antibodies tailored to specific biological and biomedical assays. They envisage Antibodypedia as a virtual repository of validated antibodies against all human, and ultimately most model-organism, proteins. Such a tool will be exploitable to identify affinity reagents to document protein expression patterns in normal and pathological states and to purify proteins alone and in complex for structural and functional analyses. They hope to promote characterization of the roles and interplay of proteins and complexes in human health and disease. They encourage commercial providers to submit information regarding their inventory of antibodies with links to quality control data. Independent users can submit their own application-specific experimental data using standard validation criteria (supportive or non-supportive) developed with the assistance of an international advisory board recruited from academic research institutions. Users can also comment on specific antibodies without submitting validation data. | cell biology, antibody, protein, human, reagent, model organism, non-human primate, FASEB list |
is listed by: 3DVC is listed by: OMICtools is related to: Nature Publishing Group |
Antibodypedia AB ; Nature Publishing Group ; European Union 6th framework - ProteomeBinders ; Human Antibody Initiative ; HUPO - Human Proteome Organisation |
PMID:18667413 PMID:18767878 |
The community can contribute to this resource | nif-0000-22918, OMICS_01770 | SCR_012782 | Antibodypedia / Nature | 2026-09-12 01:02:08 | 45 | ||||||
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e-Driver Resource Report Resource Website 1+ mentions |
e-Driver (RRID:SCR_002674) | software application, software resource, standalone software | Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes. | Identify cancer driver genes, candidate driver genes, perl, protein, mutated proteins, cancer somatic mutations, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | PMID:25064568 | Free, Available for download, Freely available | biotools:e-Driver, OMICS_05288 | https://bio.tools/e-Driver | SCR_002674 | 2026-09-12 01:02:29 | 5 | ||||||
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MapMan Resource Report Resource Website 1000+ mentions |
MapMan (RRID:SCR_003543) | MapMan | software application, software resource | Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes. | metabolic pathway, biological process, genomics, pathway, array, visualization, gene, transcript, protein, enzyme, metabolite |
is related to: GoMapMan has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany |
PMID:19389052 PMID:14996223 PMID:16009995 PMID:16649112 |
nlx_157682 | SCR_003543 | MapMan Application Software | 2026-09-12 01:02:30 | 1251 | |||||||
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VAGrENT Resource Report Resource Website 10+ mentions |
VAGrENT (RRID:SCR_005180) | VAGrENT | software resource, software toolkit | Software tool set for calculating the biological consequences of genomic variations. The suite of perl modules compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript / protein as well as Sequence Ontology terms to classify its consequences. | perl, genomic variation, transcript, mrna, cds, protein sequence, protein, sequence |
is listed by: OMICtools is related to: SO has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00192 | SCR_005180 | VAGrENT: Variation Annotation Generator, Variation Annotation Generator | 2026-09-12 01:02:34 | 17 | ||||||||
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I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France Resource Report Resource Website |
I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France (RRID:SCR_006991) | I3-CRB | biomaterial supply resource, material resource | Project to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R��seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC''''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy. | plant, animal, human, micro-organism, microorganism, bacteria, dna, protein, cell, tissue, blood, serum, organism, research |
is listed by: One Mind Biospecimen Bank Listing is related to: MeSH has parent organization: University of Lyon; France |
GIS IBiSA | Varying: Access to biological samples is provided by the participating BRC''''s., The community can contribute to this resource | nlx_36068 | SCR_006991 | Infrastructure Informatique Interop��rable pour les CRB | 2026-09-12 01:02:36 | 0 | ||||||
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TraDES Resource Report Resource Website 1+ mentions |
TraDES (RRID:SCR_006142) | TraDES | software application, software resource | With Trajectory Directed Ensemble Sampling (TraDES) create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded. TraDES is a system for directly controlling and sampling protein conformational space. TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments. The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are: * trades - generates protein structures following the Trajectory Distribution (see below) * seq2trj - makes Trajectory Distributions from sequences for sampling * str2tr - makes Trajectory Distributions from 3D structures for sampling Trajectory Distributions - Controlling the Sampling of Conformational Space The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. NMR scientists are the primary users of the TraDES package. | protein, protein structure, structure, trajectory, sequence, protein folding | has parent organization: Christopher Hogues Research Lab at the National University of Singapore | PMID:11746699 PMID:10737933 |
Open-source | nlx_151632 | SCR_006142 | Trajectory Directed Ensemble Sampling, TraDES - Trajectory Directed Ensemble Sampling | 2026-09-12 01:02:35 | 8 | ||||||
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SYFPEITHI: A Database for MHC Ligands and Peptide Motifs Resource Report Resource Website 100+ mentions |
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) | SYFPEITHI | data or information resource, database | SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713. | epitope, allele, allelic, amino acid, ape, bind, cattle, chicken, class i, class ii, human, immunological database, ligand, mhc, molecule, motif, mouse, natural, organism, peptide, product, protein, sequence, specie, t-cell, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
nif-0000-21383, biotools:syfpeithi | https://bio.tools/syfpeithi | SCR_013182 | SYFPEITHI | 2026-09-12 01:02:10 | 269 | |||||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | data or information resource, database | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-09-12 01:02:10 | 3 | ||||||
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Alzforum Antibody Directory for Neuroscience Research Resource Report Resource Website |
Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) | data or information resource, database | The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations. | alzheimer, antibody, clinical trail, community, data, disease, disorder, molecule, neurodegenerative, protein, reagent, research, science, scientific, technology | has parent organization: Alzheimer's Research Forum | nif-0000-00129 | SCR_013601 | Alzforum Antibody Directory | 2026-09-12 01:02:12 | 0 | |||||||||
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iPTMnet Resource Report Resource Website 10+ mentions |
iPTMnet (RRID:SCR_014416) | data or information resource, database | A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies. | database, protein, phosphorylation, bioinformatics, text mining, ontology | NSF ABI-1062520 | Available to the research community | SCR_014416 | 2026-09-12 01:02:14 | 31 | ||||||||||
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Glycosylation Pathways Database Resource Report Resource Website 500+ mentions |
Glycosylation Pathways Database (RRID:SCR_013486) | data or information resource, database | A pathway-based graphical interface for navigating the glycoenzyme database. The goal of the project is to define the paradigms by which carbohydrate binding proteins function in cellular communication. These pages are divided into six categories: -Glycosphingolipid: Sub-categories are Isogloboseries, Globoseries, Neo-lactoseries, Lactoseries and Ganglioseries - N-linked: Sub-categories are High-mannose, Hybrid and Complex -Mucin -Terminal Core 1 -Other O-linked -Terminal All: Includes all potential terminal structures for each glycan category | binding, carbohydrate, glycoenzyme, glycosylation, pathway, protein | NIGMS | nif-0000-20850 | SCR_013486 | GTDB | 2026-09-12 01:02:12 | 859 | |||||||||
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Therapeutically Relevant Multiple Pathways Database Resource Report Resource Website 1+ mentions |
Therapeutically Relevant Multiple Pathways Database (RRID:SCR_013471) | data or information resource, database | The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore. | drug, gene, condition, disease, intermolecular interactions and signaling pathways databases, ligand, literature, location, pathway, protein, sequence, specie, target, therapeutic, therapy | nif-0000-21402 | SCR_013471 | TRMP | 2026-09-12 01:02:12 | 3 |
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