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{ "count": 1108, "next": "?page=2", "previous": null, "list": [ { "name": "clinod", "description": "The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.\nThe predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.\nPlease note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.", "homepage": "https://www.compbio.dundee.ac.uk/www-nod/cli_help.jsp", "biotoolsID": "clinod", "biotoolsCURIE": "biotools:clinod", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "paulzierep", "additionDate": "2024-03-12T13:48:56.972279Z", "lastUpdate": "2024-03-12T13:48:56.975036Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "lorikeet", "description": "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)", "homepage": "https://github.com/AbeelLab/lorikeet", "biotoolsID": "lorikeet", "biotoolsCURIE": "biotools:lorikeet", "version": [ "20" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-12T10:56:44.977314Z", "lastUpdate": "2024-03-12T10:56:44.980036Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BBTools", "description": "BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version 7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.\n\nBBTools is open source and free for unlimited use, and is used regularly by DOE JGI and other institutions around the world.", "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/", "biotoolsID": "bbtools", "biotoolsCURIE": "biotools:bbtools", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "paulzierep", "additionDate": "2024-03-12T09:39:30.275596Z", "lastUpdate": "2024-03-12T09:39:30.279447Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "INPS-MD", "description": "Predicting the impact of mutations on protein stability from sequence and structure.", "homepage": "http://inpsmd.biocomp.unibo.it", "biotoolsID": "inps-md", "biotoolsCURIE": "biotools:inps-md", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability from sequence.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1008", "term": "Polypeptide chain ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability from structure.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Rare Disease", "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://inpsmd.biocomp.unibo.it/inpsSuite", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv291", "pmid": "25957347", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS: Predicting the impact of non-synonymous variations on protein stability from sequence", "abstract": "Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences. Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.", "date": "2015-02-06T00:00:00Z", "citationCount": 94, "authors": [ { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Savojardo C." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btw192", "pmid": "27153629", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS-MD: A web server to predict stability of protein variants from sequence and structure", "abstract": "Motivation: Protein function depends on its structural stability. The effects of single point variations on protein stability can elucidate the molecular mechanisms of human diseases and help in developing new drugs. Recently, we introduced INPS, a method suited to predict the effect of variations on protein stability from protein sequence and whose performance is competitive with the available state-of-the-art tools. Results: In this article, we describe INPS-MD (Impact of Non synonymous variations on Protein Stability-Multi-Dimension), a web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure. Here, we complement INPS with a new predictor (INPS3D) that exploits features derived from protein 3D structure. INPS3D scores with Pearson's correlation to experimental ΔΔG values of 0.58 in cross validation and of 0.72 on a blind test set. The sequence-based INPS scores slightly lower than the structure-based INPS3D and both on the same blind test sets well compare with the state-of-the-art methods.", "date": "2016-08-15T00:00:00Z", "citationCount": 147, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "savojard@biocomp.unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Piero Fariselli", "email": "piero.fariselli@unito.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Castrense Savojardo", "email": "savojard@biocomp.unibo.it", "url": "http://biocomp.unibo.it/savojard/", "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2016-05-04T15:36:53Z", "lastUpdate": "2024-03-11T16:56:00.844792Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "legsta", "description": "Performs in silico Legionella pneumophila sequence based typing", "homepage": "https://github.com/tseemann/legsta", "biotoolsID": "legsta", "biotoolsCURIE": "biotools:legsta", "version": [ "0.5.1", "0.3.7", "0.3.2", "0.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-11T16:40:14.136794Z", "lastUpdate": "2024-03-11T16:40:14.139298Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "kofamscan", "description": "KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.", "homepage": "https://github.com/takaram/kofam_scan", "biotoolsID": "kofamscan", "biotoolsCURIE": "biotools:kofamscan", "version": [ "1.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-11T15:00:11.214878Z", "lastUpdate": "2024-03-11T15:00:11.219298Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PlasFlow", "description": "PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.", "homepage": "https://github.com/smaegol/PlasFlow", "biotoolsID": "plasflow", "biotoolsCURIE": "biotools:plasflow", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-11T13:25:13.344697Z", "lastUpdate": "2024-03-11T13:25:32.934504Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Deep-AVPiden", "description": "A separable temporal convolutional networks based deep learning technique for discovering antiviral medicines.\nThe model behind this app is based on Temporal Convolutional Network (TCN). It uses the amino acid sequences of a given peptide as input and predicts whether the peptide is antifungal or not. The model consists of a word embedding layer, a spatial dropout layer, two TCN blocks, a global average pooling layer, a dense layer, and a dropout layer.", "homepage": "https://deep-avpiden.anvil.app", "biotoolsID": "deep-avpiden", "biotoolsCURIE": "biotools:deep-avpiden", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3938", "term": "Virtual screening" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41598-023-40922-Y", "pmid": "37608092", "pmcid": "PMC10444765", "type": [], "version": null, "note": null, "metadata": { "title": "A separable temporal convolutional networks based deep learning technique for discovering antiviral medicines", "abstract": "An alarming number of fatalities caused by the COVID-19 pandemic has forced the scientific community to accelerate the process of therapeutic drug discovery. In this regard, the collaboration between biomedical scientists and experts in artificial intelligence (AI) has led to a number of in silico tools being developed for the initial screening of therapeutic molecules. All living organisms produce antiviral peptides (AVPs) as a part of their first line of defense against invading viruses. The Deep-AVPiden model proposed in this paper and its corresponding web app, deployed at https://deep-avpiden.anvil.app , is an effort toward discovering novel AVPs in proteomes of living organisms. Apart from Deep-AVPiden, a computationally efficient model called Deep-AVPiden (DS) has also been developed using the same underlying network but with point-wise separable convolutions. The Deep-AVPiden and Deep-AVPiden (DS) models show an accuracy of 90% and 88%, respectively, and both have a precision of 90%. Also, the proposed models were statistically compared using the Student’s t-test. On comparing the proposed models with the state-of-the-art classifiers, it was found that they are much better than them. To test the proposed model, we identified some AVPs in the natural defense proteins of plants, mammals, and fishes and found them to have appreciable sequence similarity with some experimentally validated antimicrobial peptides. These AVPs can be chemically synthesized and tested for their antiviral activity.", "date": "2023-12-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Singh V." }, { "name": "Singh S.K." } ], "journal": "Scientific Reports" } } ], "credit": [ { "name": "Vishakha Singh", "email": "vishakhasingh.rs.cse20@iitbhu.ac.in", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sanjay Kumar Singh", "email": "sks.cse@iitbhu.ac.in", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-02-25T14:24:16.153524Z", "lastUpdate": "2024-02-25T14:24:16.156284Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Wise2.4", "description": "Compare a protein sequences or protein HMMs to a genomic DNA sequence, allowing for introns and frameshifting errors.", "homepage": "http://www.ebi.ac.uk/Tools/Wise2/", "biotoolsID": "wise", "biotoolsCURIE": "biotools:wise", "version": [ "2.4.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "HMMs" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" } ], "operatingSystem": [ "Linux" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/wise-2-2-0-compare-protein-sequence-genomic-dna-sequence.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://www.ebi.ac.uk/~birney/wise2/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/gr.10.4.547", "pmid": "10779496", "pmcid": "PMC310858", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Using GeneWise in the Drosophila annotation experiment", "abstract": "The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP) showed that GeneWise provided reasonably accurate gene predictions. Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights.", "date": "2000-04-01T00:00:00Z", "citationCount": 283, "authors": [ { "name": "Birney E." }, { "name": "Durbin R." } ], "journal": "Genome Research" } }, { "doi": null, "pmid": "15123596", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "GeneWise and Genomewise", "abstract": "We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence. ©2004 by Cold Spring Harbor Laboratory Press.", "date": "2004-05-01T00:00:00Z", "citationCount": 1775, "authors": [ { "name": "Birney E." }, { "name": "Clamp M." }, { "name": "Durbin R." } ], "journal": "Genome Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://www.ebi.ac.uk/support/index.php", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ewan Birney", "email": "birney@ebi.ac.uk", "url": null, "orcidid": "http://orcid.org/0000-0001-8314-8497", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "mbs_import", "additionDate": "2017-12-18T00:14:19Z", "lastUpdate": "2024-02-22T10:19:57.092379Z", "editPermission": { "type": "group", "authors": [ "jdispatcher" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GPCRsclass", "description": "Tool for predicting amine-binding receptors based on a protein sequence provided by the user.", "homepage": "http://webs.iiitd.edu.in/raghava/gpcrsclass/", "biotoolsID": "gpcrsclass", "biotoolsCURIE": "biotools:gpcrsclass", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0269", "term": "Transmembrane protein prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "gpcr" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://webs.iiitd.edu.in/raghava/gpcrsclass/help.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "15980444", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "GPCRsclass: A web tool for the classification of amine type of G-protein-coupled receptors", "abstract": "The receptors of amine subfamily are specifically major drug targets for therapy of nervous disorders and psychiatric diseases. The recognition of novel amine type of receptors and their cognate ligands is of paramount interest for pharmaceutical companies. In the past, Chou and co-workers have shown that different types of amine receptors are correlated with their amino acid composition and are predictable on its basis with considerable accuracy [Elrod and Chou (2002) Protein Eng., 15, 713-715]. This motivated us to develop a better method for the recognition of novel amine receptors and for their further classification. The method was developed on the basis of amino acid composition and dipeptide composition of proteins using support vector machine. The method was trained and tested on 167 proteins of amine subfamily of G-protein-coupled receptors (GPCRs). The method discriminated amine subfamily of GPCRs from globular proteins with Matthew's correlation coefficient of 0.98 and 0.99 using amino acid composition and dipeptide composition, respectively. In classifying different types of amine receptors using amino acid composition and dipeptide composition, the method achieved an accuracy of 89.8 and 96.4%, respectively. The performance of the method was evaluated using 5-fold cross-validation. The dipeptide composition based method predicted 67.6% of protein sequences with an accuracy of 100% with a reliability index ≥5. A web server GPCRsclass has been developed for predicting amine-binding receptors from its amino acid sequence [http://www.imtech.res.in/raghava/gpcrsclass/ and http://bioinformatics.uams.edu/raghava/gpersclass/ (mirror site)]. © 2005 Oxford University Press.", "date": "2005-07-01T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Bhasin M." }, { "name": "Raghava G.P.S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "G.P.S. Raghava", "email": "raghava@iiitd.ac.in", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Prof Raghava is know to develop open source in bioinformatics" } ], "community": null, "owner": "raghavagps", "additionDate": "2017-02-10T14:15:37Z", "lastUpdate": "2024-02-15T12:37:17.336664Z", "editPermission": { "type": "group", "authors": [ "mbermudez1" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }