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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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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 | SciCrunch Registry | SYFPEITHI | 2026-10-24 12:51:05 | 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 | SciCrunch Registry | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-10-24 12:51:05 | 3 | ||||||
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UniCarbKB Resource Report Resource Website 10+ mentions |
UniCarbKB (RRID:SCR_014410) | data or information resource, database | International effort which has created a glycomics knowledgebase with access to a database of information on the glycan structures of glycoproteins. It serves as and promotes an online information storage and search platform for glycomics and glycobiology research. Open access knowledgebase offers resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data. | knowledgebase, glycomics, glycerin structure, glycoprotein, cell line, glycoproteomics knowledge platform, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Macquarie University; Sydney; Australia has parent organization: University of Gothenburg; Gothenburg; Sweden has parent organization: SIB Swiss Institute of Bioinformatics is parent organization of: UniCarb-DB |
DOI:10.1093/nar/gkt1128 | Free, Freely available | biotools:unicarbkb | https://bio.tools/unicarbkb | http://www.unicarbkb.org | SCR_014410 | SciCrunch Registry | 2026-10-24 12:51:09 | 28 | ||||||
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ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | data or information resource, database | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb, r3d100012265 | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | SciCrunch Registry | CryptoDB, Cryptosporidium Genomics Resource | 2026-10-24 12:51:08 | 26 | ||||
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SnpSift Resource Report Resource Website 500+ mentions |
SnpSift (RRID:SCR_015624) | software resource, software toolkit, source code | Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files. | annotation, filtering, genomic variant, single nucleotide polymorphism, bio.tools |
is listed by: bio.tools is listed by: Debian works with: SnpEff |
PMID:22728672 | Open Source, Free, Available for download | biotools:snpsift | https://bio.tools/snpsift | SCR_015624 | SciCrunch Registry | SnpEff | 2026-10-24 12:51:13 | 631 | ||||||
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Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | data or information resource, database | Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally. | clinical trial, clinical trial database, clinical trial data, open database, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
Laura and John Arnold Foundation ; Wellcome Trust ; World Health Organisation ; West of England Academic Health Science Network |
Open source | biotools:opentrials | https://bio.tools/opentrials | SCR_015570 | SciCrunch Registry | 2026-10-24 12:51:13 | 3 | |||||||
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Genome Aggregation Database Resource Report Resource Website 5000+ mentions |
Genome Aggregation Database (RRID:SCR_014964) | gnomAD | data or information resource, database | Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. | database, genome, , bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute Genomics Platform has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
Broad Institute | Open source, Available to the biomedical community, The community can contribute to this resource | biotools:gnomad | https://github.com/macarthur-lab/gnomad_browser/issues, https://bio.tools/gnomad | SCR_014964 | SciCrunch Registry | gnomAD 2.0, gnomAD Browser, gnomAD version 2.0, Exome Aggregation Consortium | 2026-10-24 12:51:10 | 5310 | |||||
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Examl Resource Report Resource Website 50+ mentions |
Examl (RRID:SCR_016087) | Examl | software application, software resource, source code | Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers. | phylogenetic, analysis, database, large scale, whole genome, whole transcriptome, alignment, efficiency, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Heidelberg Institute for Theoretical Studies | PMID:25819675 | Free, Available for download | OMICS_08024, biotools:ExaML | https://bio.tools/ExaML, https://sources.debian.org/src/examl/ | SCR_016087 | SciCrunch Registry | Examl:Exascale Maximum Likelihood | 2026-10-24 12:51:14 | 62 | ||||
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lncRNAdb Resource Report Resource Website 100+ mentions |
lncRNAdb (RRID:SCR_015491) | data or information resource, database | Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature. | reference database, eukaryotic annotation, annotation database, eukaryotic long non coding rna database, functional long noncoding rnas, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
Open source, Acknowledgement requested, The community can contribute to this resource | biotools:lncrnadb | https://bio.tools/lncrnadb | SCR_015491 | SciCrunch Registry | lncRNAdb v2.0, Long Noncoding RNA Database, Long Noncoding RNA Database v2.0 | 2026-10-24 12:51:10 | 165 | |||||||
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ExPASy ABCD database Resource Report Resource Website 10+ mentions |
ExPASy ABCD database (RRID:SCR_017401) | ABCD ExPASy, The ABCD database | data or information resource, database | Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments. | Sequenced antibody, manually curated, known target, ExPASy, repository, chemically defined antibodies, antibody, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: SIB Swiss Institute of Bioinformatics has parent organization: University of Geneva; Geneva; Switzerland |
ProCare Foundation ; Swiss National Science Foundation ; University of Geneva |
PMID:31410491 | Free, Freely available | SCR_019000, biotools:AbCD_database | https://bio.tools/ABCD_database | SCR_017401 | SciCrunch Registry | ExPASy ABCD (AntiBodies Chemically Defined) Database, The ABCD database, AntiBodies Chemically Defined, AntiBodies Chemically Defined Expert Protein Analysis System database, ExPASy ABCD Database, The AntiBodies Chemically Defined Database | 2026-10-24 12:51:12 | 13 | ||||
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MethBase Resource Report Resource Website 1+ mentions |
MethBase (RRID:SCR_017487) | data or information resource, database, service resource | Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics. | Methylome, database, public, BSseq, dataset, methylation, site, region, allele, specific, metadata, statistics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
Free, Freely available | BioTools:MethBase, biotools:Methbase | https://bio.tools/MethBase, https://bio.tools/MethBase, https://bio.tools/MethBase | SCR_017487 | SciCrunch Registry | MethBase: a reference methylome database | 2026-10-24 12:51:13 | 1 | |||||||
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Signaling Pathways Project Resource Report Resource Website 10+ mentions |
Signaling Pathways Project (RRID:SCR_018412) | SPP | data or information resource, database | Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available. | Data integration, genetic database, gene regulatory network, cell signalling, cellular signalling network, transcriptomic data, manualy curated, cistromic data, cellular receptor, enzyme, transcrptomic factor, mammalian cellular signaling pathway, data mining strategy, dataset, , bio.tools |
is used by: Hypothesis Center is listed by: Debian is listed by: bio.tools works with: Gene Expression Omnibus (GEO) works with: NCBI Sequence Read Archive (SRA) |
CPRIT RP150578; Dan L. Duncan NCI Comprehensive Cancer Center at Baylor College of Medicine ; NCI CA125123; NHLBI HL127624; NIDDK DK095686; NIDDK DK097748; NIDDK DK097771; NIDDK DK105126; NIDDK DK107535; NIDDK DK48807; NIDDK DK56338 |
PMID:31672983 | Free, Freely available | r3d100013650, biotools:Signaling_Pathways_Project | https://bio.tools/Signaling_Pathways_Project, https://doi.org/10.17616/R31NJN0Y | https://www.signalingpathways.org | SCR_018412 | SciCrunch Registry | 2026-10-24 12:51:13 | 34 | ||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | SciCrunch Registry | 2026-10-24 12:50:38 | 3 | ||||||
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HMM-TM Resource Report Resource Website 1+ mentions |
HMM-TM (RRID:SCR_006186) | HMM-TM | analysis service resource, data analysis service, production service resource, service resource | A web tool using the Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information. Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature. We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM''s classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications. | hidden markov model, topology, prediction, alpha-helical membrane protein, protein, transmembrane, transmembrane alpha-helical protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:16597327 | Free for academic use | nlx_151731, biotools:hmm-tm | https://bio.tools/hmm-tm | SCR_006186 | SciCrunch Registry | HMM-TM: Prediction of Transmembrane Alpha-Helical Proteins | 2026-10-24 12:50:38 | 7 | |||||
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PRED-LIPO Resource Report Resource Website 10+ mentions |
PRED-LIPO (RRID:SCR_006187) | PRED-LIPO | analysis service resource, data analysis service, production service resource, service resource | A web tool using the Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods based on regular expression patterns, in various data sets containing experimentally characterized lipoproteins, secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins. The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides. | hidden markov model, lipoprotein signal peptide, gram-positive bacteria, lipoprotein, prediction, peptide, protein, signal peptide, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
National Scholarships Foundation of Greece | PMID:19367716 | Free | nlx_151732, biotools:pred-lipo | https://bio.tools/pred-lipo | SCR_006187 | SciCrunch Registry | PRED-LIPO: Prediction of Lipoprotein and Secretory Signal Peptides in Gram-positive Bacteria with Hidden Markov Models | 2026-10-24 12:50:38 | 17 | ||||
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PRED-SIGNAL Resource Report Resource Website 10+ mentions |
PRED-SIGNAL (RRID:SCR_006181) | PRED-SIGNAL | analysis service resource, data analysis service, production service resource, service resource | A web tool for prediction of signal peptides in archaea. Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones. | signal peptide, prediction, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
State Scholarships Foundation of Greece | PMID:18988691 | Free for academic use | biotools:pred-signal, nlx_151728 | https://bio.tools/pred-signal | SCR_006181 | SciCrunch Registry | PRED-SIGNAL - Prediction of Signal Peptides in Archaea with Hidden Markov Models | 2026-10-24 12:50:38 | 14 | ||||
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SILVA Resource Report Resource Website 10000+ mentions |
SILVA (RRID:SCR_006423) | data or information resource, database | High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online. | ribosomal rna, gene sequence, gene, sequence, alignment, taxonomy, 16s, 18s, 23s, 28s, phylogeny, probe, primer, alignment service, fish, arb, ribocon, geoblast, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: RNAcentral is related to: ARB project is related to: SINA is related to: European ribosomal RNA database has parent organization: German Collection of Microorganisms and Cell Cultures |
German Collection of Microorganisms and Cell Cultures | PMID:23193283 PMID:24293649 PMID:17947321 |
biotools:silva, OMICS_01514, nif-0000-03464, r3d100011323, rid_000103 | https://bio.tools/silva, https://doi.org/10.17616/R3FP60 | SCR_006423 | SciCrunch Registry | SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-10-24 12:50:39 | 15971 | ||||||
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ViralZone Resource Report Resource Website 100+ mentions |
ViralZone (RRID:SCR_006563) | ViralZone | data or information resource, database | ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ViralZone project is handled by the virus program of SwissProt group. Proteins popups were developed in collaboration with Prof. Christian von Mering and Andrea Franceschini, Bioinformatics Group , Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, funded in part by the SIB Swiss Institute of bioinformatics. All pictures in ViralZone are copyright of the SIB Swiss Institute of Bioinformatics. | dna virus, rna virus, virus, dna, rna, genomic, proteomic, sequence, reference strain, image, virion, retro-transcribing virus, genome, bibliographic, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Institute of Bioinformatics | PMID:20947564 | biotools:viralzone, r3d100013314, nlx_144372 | https://bio.tools/viralzone, https://doi.org/10.17616/R31NJMRM | http://www.expasy.org/viralzone/ | SCR_006563 | SciCrunch Registry | Viral Zone | 2026-10-24 12:50:39 | 148 | ||||
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neuroelectro Resource Report Resource Website 10+ mentions |
neuroelectro (RRID:SCR_006274) | NeuroElectro | data or information resource, database | A database of elecrophysiological properties text-mined from the biomedical literature as a function of neuron type. Specifically, NeuroElectro seeks to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database. There are 252 neurons currently available, with the naming convention established in NeuroLex. | electrophysiology, text mining, cellular neurophysiology, neuron, neuron electrophysiology, bio.tools |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: NeuroLex has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Open unspecified license | nlx_151885, BioTools:neuroelectro, biotools:neuroelectro, r3d100011798 | https://bio.tools/neuroelectro, https://bio.tools/neuroelectro, https://bio.tools/neuroelectro, https://doi.org/10.17616/R3BP7F | SCR_006274 | SciCrunch Registry | Neuro Electro, NeuroElectro: organizing information on cellular neurophysiology | 2026-10-24 12:50:38 | 27 | ||||||
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Scansite Resource Report Resource Website 100+ mentions |
Scansite (RRID:SCR_007026) | data or information resource, database | Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. The Motifscanner program utilizes an entropy approach that assesses the probability of a site matching the motif using the selectivity values and sums the logs of the probability values for each amino acid in the candidate sequence. The program then indicates the percentile ranking of the candidate motif in respect to all potential motifs in proteins of a protein database. When available, percentile scores of some confirmed phosphorylation sites for the kinase of interests or confirmed binding sites of the domain of interest are provided for comparison with the scores of the candidate motifs. | binding, kinase, phosphorylate, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
biotools:scansite, nif-0000-20914 | https://bio.tools/scansite | SCR_007026 | SciCrunch Registry | Scansite | 2026-10-24 12:50:41 | 302 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
