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{ "count": 272, "next": "?page=2", "previous": null, "list": [ { "name": "Proteinortho", "description": "Proteinortho is a tool to detect orthologous genes within different species", "homepage": "https://www.bioinf.uni-leipzig.de/Software/proteinortho/", "biotoolsID": "proteinortho", "biotoolsCURIE": "biotools:proteinortho", "version": [ "6.0.14" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3663", "term": "Homology-based gene prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Perl", "C++", "Python" ], "license": "GPL-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/paulklemm_PHD/proteinortho", "type": [ "Repository" ], "note": null }, { "url": "https://gitlab.com/paulklemm_PHD/proteinortho/-/issues?sort=created_date&state=opened", "type": [ "Issue tracker" ], "note": null }, { "url": "https://toolshed.g2.bx.psu.edu/repository?repository_id=584d8accff31aefe&changeset_revision=4850f0d15f01", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip", "type": "Source code", "note": null, "version": null }, { "url": "https://packages.debian.org/unstable/proteinortho", "type": "Downloads page", "note": "Installation with dpkg (root privileges are required)", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1186/1471-2105-12-124", "pmid": "21526987", "pmcid": "PMC3114741", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Proteinortho: Detection of (Co-)orthologs in large-scale analysis", "abstract": "Background: Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases.Results: The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes.Conclusions: Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware. © 2011 Lechner et al; licensee BioMed Central Ltd.", "date": "2011-04-28T00:00:00Z", "citationCount": 656, "authors": [ { "name": "Lechner M." }, { "name": "Findeiss S." }, { "name": "Steiner L." }, { "name": "Marz M." }, { "name": "Stadler P.F." }, { "name": "Prohaska S.J." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Marcus Lechner", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Sonja J Prohaska", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "klemmp", "additionDate": "2022-03-22T18:57:49.937151Z", "lastUpdate": "2024-03-12T09:10:35.206389Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SVMyr", "description": "A Web Server Detecting Co- and Post-translational Myristoylation in Proteins.", "homepage": "https://busca.biocomp.unibo.it/lipipred", "biotoolsID": "svmyr", "biotoolsCURIE": "biotools:svmyr", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "PTM site prediction" }, { "uri": "http://edamontology.org/operation_0422", "term": "Protein cleavage site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "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" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://busca.biocomp.unibo.it/lipipred/about/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/J.JMB.2022.167605", "pmid": "35662454", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SVMyr: A Web Server Detecting Co- and Post-translational Myristoylation in Proteins", "abstract": "Myristoylation (MYR) is a protein modification where a myristoyl group is covalently attached to an exposed (N-terminal) glycine residue. Glycine myristoylation occurs during protein translation (co-translation) or after (post-translation). Myristoylated proteins have a role in signal transduction, apoptosis, and pathogen-mediated processes and their prediction can help in functionally annotating the fraction of proteins undergoing MYR in different proteomes. Here we present SVMyr, a web server allowing the detection of both co- and post-translational myristoylation sites, based on Support Vector Machines (SVM). The input encodes composition and physicochemical features of the octapeptides, known to act as substrates and to physically interact with N-myristoyltransferases (NMTs), the enzymes catalyzing the myristoylation reaction. The method, adopting a cross validation procedure, scores with values of Area Under the Curve (AUC) and Matthews Correlation Coefficient (MCC) of 0.92 and 0.61, respectively. When benchmarked on an independent dataset including experimentally detected 88 medium/high confidence co-translational myristoylation sites and 528 negative examples, SVMyr outperforms available methods, with AUC and MCC equal to 0.91 and 0.58, respectively. A unique feature of SVMyr is the ability to predict post-translational myristoylation sites by coupling the trained SVMs with the detection of caspase cleavage sites, identified by searching regular motifs matching upstream caspase cleavage sites, as reported in literature. Finally, SVMyr confirms 96% of the UniProt set of the electronically annotated myristoylated proteins (31,048) and identifies putative myristoylomes in eight different proteomes, highlighting also new putative NMT substrates. SVMyr is freely available through a user-friendly web server at https://busca.biocomp.unibo.it/lipipred.", "date": "2022-06-15T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Madeo G." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2022-09-01T11:34:17.973845Z", "lastUpdate": "2024-03-11T16:39:58.647418Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CoCoNat", "description": "CoCoNat is a novel deep-learning based method for predicting coiled-coil regions, register annotation and oligomenrization state. CoCoNat adopts a sequence encoding based on two state-of-the-art protein language models and a deep-learning architetcure to perform prediction.", "homepage": "https://coconat.biocomp.unibo.it", "biotoolsID": "coconat", "biotoolsCURIE": "biotools:coconat", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0268", "term": "Protein super-secondary structure prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "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" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/coconat", "type": "Source code", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/coconat", "type": [ "Command-line options" ], "note": null }, { "url": "https://coconat.biocomp.unibo.it/help/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad495", "pmid": "37540220", "pmcid": "PMC10425188", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CoCoNat: a novel method based on deep learning for coiled-coil prediction", "abstract": "Motivation: Coiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction methods include the precise identification of CCD boundaries, the annotation of the typical heptad repeat pattern along the coiled-coil helices as well as the prediction of the oligomerization state. Results: In this article, we describe CoCoNat, a novel method for predicting coiled-coil helix boundaries, residue-level register annotation, and oligomerization state. Our method encodes sequences with the combination of two state-of-the-art protein language models and implements a three-step deep learning procedure concatenated with a Grammatical-Restrained Hidden Conditional Random Field for CCD identification and refinement. A final neural network predicts the oligomerization state. When tested on a blind test set routinely adopted, CoCoNat obtains a performance superior to the current state-of-the-art both for residue-level and segment-level CCD. CoCoNat significantly outperforms the most recent state-of-the-art methods on register annotation and prediction of oligomerization states.", "date": "2023-08-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Madeo G." }, { "name": "Savojardo C." }, { "name": "Manfredi M." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.21769/BioProtoc.4935", "pmid": "38405078", "pmcid": "PMC10883893", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "CoCoNat: A Deep Learning–Based Tool for the Prediction of Coiled-coil Domains in Protein Sequences", "abstract": "Coiled-coil domains (CCDs) are structural motifs observed in proteins in all organisms that perform several crucial functions. The computational identification of CCD segments over a protein sequence is of great importance for its functional characterization. This task can essentially be divided into three separate steps: the detection of segment boundaries, the annotation of the heptad repeat pattern along the segment, and the classification of its oligomerization state. Several methods have been proposed over the years addressing one or more of these predictive steps. In this protocol, we illustrate how to make use of CoCoNat, a novel approach based on protein language models, to characterize CCDs. CoCoNat is, at its release (August 2023), the state of the art for CCD detection. The web server allows users to submit input protein sequences and visualize the predicted domains after a few minutes. Optionally, precomputed segments can be provided to the model, which will predict the oligomerization state for each of them. CoCoNat can be easily integrated into biological pipelines by downloading the standalone version, which provides a single executable script to produce the output.", "date": "2024-02-20T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Manfredi M." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bio-protocol" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2024-01-28T18:03:20.705547Z", "lastUpdate": "2024-03-11T16:30:11.896748Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "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": "E-SNPs and GO", "description": "E-SNPs&GO is a machine-learning method the pathogenicity of human variations. E-SNPs&GO classify input variations into pathogenic or benign.", "homepage": "https://esnpsandgo.biocomp.unibo.it/", "biotoolsID": "E-SNPsGO", "biotoolsCURIE": "biotools:E-SNPsGO", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Other" ], "license": null, "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "https://esnpsandgo.biocomp.unibo.it/help/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btac678", "pmid": "36227117", "pmcid": "PMC9710551", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants", "abstract": "MOTIVATION: The advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing their sequences. Discriminating harmful protein variations from neutral ones is one of the crucial challenges in precision medicine. Computational tools based on artificial intelligence provide models for protein sequence encoding, bypassing database searches for evolutionary information. We leverage the new encoding schemes for an efficient annotation of protein variants. RESULTS: E-SNPs&GO is a novel method that, given an input protein sequence and a single amino acid variation, can predict whether the variation is related to diseases or not. The proposed method adopts an input encoding completely based on protein language models and embedding techniques, specifically devised to encode protein sequences and GO functional annotations. We trained our model on a newly generated dataset of 101 146 human protein single amino acid variants in 13 661 proteins, derived from public resources. When tested on a blind set comprising 10 266 variants, our method well compares to recent approaches released in literature for the same task, reaching a Matthews Correlation Coefficient score of 0.72. We propose E-SNPs&GO as a suitable, efficient and accurate large-scale annotator of protein variant datasets. AVAILABILITY AND IMPLEMENTATION: The method is available as a webserver at https://esnpsandgo.biocomp.unibo.it. Datasets and predictions are available at https://esnpsandgo.biocomp.unibo.it/datasets. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.", "date": "2022-11-30T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Manfredi M." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics (Oxford, England)" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matteo Manfredi", "email": "matteo.manfredi4@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "PierLuigiMartelli", "additionDate": "2023-01-05T08:42:10.922859Z", "lastUpdate": "2024-03-07T17:58:00.968691Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepREx", "description": "A web server for characterising protein-solvent interaction starting from sequence.", "homepage": "https://deeprex.biocomp.unibo.it", "biotoolsID": "deeprex", "biotoolsCURIE": "biotools:deeprex", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3904", "term": "Protein disorder prediction" }, { "uri": "http://edamontology.org/operation_0387", "term": "Molecular surface calculation" }, { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" } ], "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": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/BolognaBiocomp/deeprex", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/bolognabiocomp/deeprex", "type": "Container file", "note": null, "version": null }, { "url": "https://github.com/BolognaBiocomp/deeprex", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://deeprex.biocomp.unibo.it/about/tutorial/", "type": [ "User manual" ], "note": "Web application manual" }, { "url": "https://github.com/BolognaBiocomp/deeprex", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1016/J.CSBJ.2021.10.016", "pmid": "34765094", "pmcid": "PMC8566768", "type": [], "version": null, "note": null, "metadata": { "title": "DeepREx-WS: A web server for characterising protein–solvent interaction starting from sequence", "abstract": "Protein–solvent interaction provides important features for protein surface engineering when the structure is absent or partially solved. Presently, we can integrate the notion of solvent exposed/buried residues with that of their flexibility and intrinsic disorder to highlight regions where mutations may increase or decrease protein stability in order to modify proteins for biotechnological reasons, while preserving their functional integrity. Here we describe a web server, which provides the unique possibility of integrating knowledge of solvent and non-solvent exposure with that of residue conservation, flexibility and disorder of a protein sequence, for a better understanding of which regions are relevant for protein integrity. The core of the webserver is DeepREx, a novel deep learning-based tool that classifies each residue in the sequence as buried or exposed. DeepREx is trained on a high-quality, non-redundant dataset derived from the Protein Data Bank comprising 2332 monomeric protein chains and benchmarked on a blind test set including 200 protein sequences unrelated with the training set. Results show that DeepREx performs at the state-of-the-art in the field. In turn, the Web Server, DeepREx-WS, supplements the predictions of DeepREx with features that allow a better characterisation of exposed and buried regions: i) residue conservation derived from multiple sequence alignment; ii) local sequence hydrophobicity; iii) residue flexibility computed with MEDUSA; iv) a predictor of secondary structure; v) the presence of disordered regions as derived from MobiDB-Lite3.0. The web server allows browsing, selecting and intersecting the different features. We demonstrate a possible application of the DeepREx-WS for assisting the identification of residues to be variated in protein surface engineering processes.", "date": "2021-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Manfredi M." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Computational and Structural Biotechnology Journal" } }, { "doi": "10.3389/fmolb.2020.626363", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences", "abstract": "Solvent accessibility (SASA) is a key feature of proteins for determining their folding and stability. SASA is computed from protein structures with different algorithms, and from protein sequences with machine-learning based approaches trained on solved structures. Here we ask the question as to which extent solvent exposure of residues can be associated to the pathogenicity of the variation. By this, SASA of the wild-type residue acquires a role in the context of functional annotation of protein single-residue variations (SRVs). By mapping variations on a curated database of human protein structures, we found that residues targeted by disease related SRVs are less accessible to solvent than residues involved in polymorphisms. The disease association is not evenly distributed among the different residue types: SRVs targeting glycine, tryptophan, tyrosine, and cysteine are more frequently disease associated than others. For all residues, the proportion of disease related SRVs largely increases when the wild-type residue is buried and decreases when it is exposed. The extent of the increase depends on the residue type. With the aid of an in house developed predictor, based on a deep learning procedure and performing at the state-of-the-art, we are able to confirm the above tendency by analyzing a large data set of residues subjected to variations and occurring in some 12,494 human protein sequences still lacking three-dimensional structure (derived from HUMSAVAR). Our data support the notion that surface accessible area is a distinguished property of residues that undergo variation and that pathogenicity is more frequently associated to the buried property than to the exposed one.", "date": "2021-01-07T00:00:00Z", "citationCount": 51, "authors": [ { "name": "Savojardo C." }, { "name": "Manfredi M." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Frontiers in Molecular Biosciences" } } ], "credit": [ { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Rita Casadio", "email": "rita.casadio@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Matteo Manfredi", "email": "matteo.manfredi4@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2022-05-15T09:43:33.456849Z", "lastUpdate": "2024-03-07T17:57:11.201008Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BENZ WS", "description": "The Bologna ENZyme Web Server (BENZ WS) annotates the Enzyme Commission numbers (EC numbers) of enzymes. BENZ WS is based on HMMs and PFAMs and returns a four-level EC number for a target which is retained by the system.", "homepage": "https://benzdb.biocomp.unibo.it", "biotoolsID": "benz-ws", "biotoolsCURIE": "biotools:benz-ws", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://benzdb.biocomp.unibo.it/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/NAR/GKAB328", "pmid": "33963861", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BENZ WS: The Bologna ENZyme Web Server for four-level EC number annotation", "abstract": "The Bologna ENZyme Web Server (BENZ WS) annotates four-level Enzyme Commission numbers (EC numbers) as defined by the International Union of Biochemistry and Molecular Biology (IUBMB). BENZ WS filters a target sequence with a combined system of Hidden Markov Models, modelling protein sequences annotated with the same molecular function, and Pfams, carrying along conserved protein domains. BENZ returns, when successful, for any enzyme target sequence an associated four-level EC number. Our system can annotate both monofunctional and polyfunctional enzymes, and it can be a valuable resource for sequence functional annotation.", "date": "2021-07-02T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Baldazzi D." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2021-06-14T13:42:20Z", "lastUpdate": "2024-03-07T17:56:22.660972Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ISPRED-SEQ", "description": "Deep neural networks and embeddings for predicting interaction sites in protein sequences.", "homepage": "https://ispredws.biocomp.unibo.it", "biotoolsID": "ispred-seq", "biotoolsCURIE": "biotools:ispred-seq", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_3094", "term": "Protein interaction network prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_3899", "term": "Protein-protein docking" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://ispredws.biocomp.unibo.it/sequence/about/tutorial/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jmb.2023.167963", "pmid": "37356906", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ISPRED-SEQ: Deep Neural Networks and Embeddings for Predicting Interaction Sites in Protein Sequences", "abstract": "The knowledge of protein–protein interaction sites (PPIs) is crucial for protein functional annotation. Here we address the problem focusing on the prediction of putative PPIs considering as input protein sequences. The issue is important given the huge volume of protein sequences compared to experimental and/or computed structures. Taking advantage of protein language models, recently developed, and Deep Neural networks, here we describe ISPRED-SEQ, which overpasses state-of-the-art predictors addressing the same problem. ISPRED-SEQ is freely available for testing at https://ispredws.biocomp.unibo.it.", "date": "2023-07-15T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Manfredi M." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "http://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Rita Casadio", "email": "rita.casadio@unibo.it", "url": null, "orcidid": "http://orcid.org/0000-0002-7462-7039", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "http://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Matteo Manfredi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2023-03-28T22:48:48.088931Z", "lastUpdate": "2024-03-07T17:55:59.780584Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "E-pRSA", "description": "E-pRSA is a method for predicting the Relative Solvent Accessibility of residues in a protein chain without requiring previous knowledge of the 3-dimensional structure. E-pRSA is based on embeddings derived from protein language models.", "homepage": "https://e-prsa.biocomp.unibo.it/main", "biotoolsID": "e-prsa", "biotoolsCURIE": "biotools:e-prsa", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0384", "term": "Accessible surface calculation" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": null, "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://e-prsa.biocomp.unibo.it/main/about/tutorial/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jmb.2024.168494", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matteo Manfredi", "email": "matteo.manfredi4@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Support" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2024-03-07T16:59:02.773893Z", "lastUpdate": "2024-03-07T17:02:02.229706Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BetAware-Deep", "description": "BetAware-Deep is web server for predicting the topology of TransMembrane Beta-Barrel (TMBB) proteins in Gram-negative bacteria.", "homepage": "https://busca.biocomp.unibo.it/betaware2/", "biotoolsID": "betaware-deep", "biotoolsCURIE": "biotools:betaware-deep", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "betaware", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0269", "term": "Transmembrane protein prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0820", "term": "Membrane and lipoproteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://busca.biocomp.unibo.it/betaware2/help/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jmb.2020.166729", "pmid": "33972021", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins", "abstract": "TransMembrane β-Barrel (TMBB) proteins located in the outer membranes of Gram-negative bacteria are crucial for many important biological processes and primary candidates as drug targets. Structure determination of TMBB proteins is challenging and hence computational methods devised for the analysis of TMBB proteins are important for complementing experimental approaches. Here, we present a novel web server called BetAware-Deep that is able to accurately identify the topology of TMBB proteins (i.e. the number and orientation of membrane-spanning segments along the protein sequence) and to discriminate them from other protein types. The method in BetAware-Deep defines new features by exploiting a non-canonical computation of the hydrophobic moment and by adopting sequence-profile weighting of the White&Wimley hydrophobicity scale. These features are processed using a two-step approach based on deep learning and probabilistic graphical models. BetAware-Deep has been trained on a dataset comprising 58 TMBBs and benchmarked on a novel set of 15 TMBB proteins. Results showed that BetAware-Deep outperforms two recently released state-of-the-art methods for topology prediction, predicting correct topologies of 10 out of 15 proteins. TMBB detection was also assessed on a larger dataset comprising 1009 TMBB proteins and 7571 non-TMBB proteins. Even in this benchmark, BetAware-Deep scored at the level of top-performing methods. A web server has been developed allowing users to analyze input protein sequences and providing topology prediction together with a rich set of information including a graphical representation of the residue-level annotations and prediction probabilities. BetAware-Deep is available at https://busca.biocomp.unibo.it/betaware2.", "date": "2021-05-28T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Madeo G." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2021-01-27T11:47:58Z", "lastUpdate": "2024-03-07T11:47:33.221761Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }