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{ "count": 43, "next": "?page=2", "previous": null, "list": [ { "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": "compareMS2", "description": "compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.", "homepage": "https://github.com/524D/compareMS2", "biotoolsID": "comparems2", "biotoolsCURIE": "biotools:comparems2", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3272", "term": "Species tree" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C", "JavaScript" ], "license": "MIT", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/524D/compareMS2", "type": [ "Repository" ], "note": null }, { "url": "https://www.ms-utils.org/compareMS2.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.html", "type": "Binaries", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://github.com/524D/compareMS2/tree/main/src", "type": "Source code", "note": null, "version": "2.0" }, { "url": "https://github.com/524D/compareMS2/tree/main", "type": "Binaries", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://www.ms-utils.org/compareMS2.html", "type": [ "General", "Command-line options" ], "note": null }, { "url": "https://github.com/524D/compareMS2", "type": [ "General", "User manual", "Command-line options", "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.6162", "pmid": "22368051", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Molecular phylogenetics by direct comparison of tandem mass spectra", "abstract": "Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.", "date": "2012-04-15T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Palmblad M." }, { "name": "Deelder A.M." } ], "journal": "Rapid Communications in Mass Spectrometry" } }, { "doi": "10.1021/acs.jproteome.2c00457", "pmid": "36173614", "pmcid": "PMC9903320", "type": [ "Other" ], "version": "2.0", "note": null, "metadata": { "title": "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets", "abstract": "It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.", "date": "2023-02-03T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Marissen R." }, { "name": "Varunjikar M.S." }, { "name": "Laros J.F.J." }, { "name": "Rasinger J.D." }, { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.1c00528", "pmid": "34523928", "pmcid": "PMC8491155", "type": [ "Review" ], "version": "2.0", "note": null, "metadata": { "title": "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics", "abstract": "Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a \"gem\"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.", "date": "2021-10-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": "https://www.lumc.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Support" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": "https://github.com/magnuspalmblad", "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Documentor" ], "note": null }, { "name": "Rob Marissen", "email": null, "url": "https://github.com/524D", "orcidid": "https://orcid.org/0000-0002-1220-9173", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "n.m.palmblad@lumc.nl", "additionDate": "2016-04-15T11:52:42Z", "lastUpdate": "2024-02-13T15:35:10.776331Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Scan", "description": "Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data", "homepage": "https://github.com/zhangjunpeng411/Scan", "biotoolsID": "Scan", "biotoolsCURIE": "biotools:Scan", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2437", "term": "Gene regulatory network prediction" }, { "uri": "http://edamontology.org/operation_3792", "term": "miRNA expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R", "MATLAB" ], "license": "AGPL-3.0", "collectionID": [ "Cancer" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/zhangjunpeng411/Scan", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/zhangjunpeng411/Scan", "type": "Source code", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://github.com/zhangjunpeng411/Scan", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Junpeng Zhang", "email": "zhangjunpeng411@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-6127-9701", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "zhangjunpeng", "additionDate": "2023-11-17T03:14:31.662275Z", "lastUpdate": "2023-11-17T07:03:20.353905Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Planet Microbe", "description": "Enabling the discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers.", "homepage": "https://www.planetmicrobe.org/", "biotoolsID": "planetmicrobe", "biotoolsCURIE": "biotools:planetmicrobe", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3387", "term": "Marine biology" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" } ], "operatingSystem": [ "Linux" ], "language": [ "Elm" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/hurwitzlab/planet-microbe-app", "type": [ "Repository" ], "note": "Planet Microbe Application" }, { "url": "https://github.com/hurwitzlab/planet-microbe-datapackages", "type": [ "Repository" ], "note": "Planet Microbe frictionless data packages" }, { "url": "https://github.com/hurwitzlab/planet-microbe-ontology", "type": [ "Repository" ], "note": "Planet Microbe ontology" }, { "url": "https://github.com/hurwitzlab/planet-microbe-functional-annotation", "type": [ "Repository" ], "note": "Functional Annotation Pipeline" }, { "url": "https://github.com/hurwitzlab/planet-microbe-semantic-web-analysis", "type": [ "Repository" ], "note": "Semantic web analysis" } ], "download": [ { "url": "https://github.com/hurwitzlab/planet-microbe-app", "type": "Source code", "note": "Source code for the website", "version": "1.0" } ], "documentation": [ { "url": "https://hurwitzlab.gitbook.io/planet-microbe-documentation/", "type": [ "General" ], "note": "Documentation on how to use the website" } ], "publication": [ { "doi": "10.1093/nar/gkaa637", "pmid": "32735679", "pmcid": "PMC7778950", "type": [ "Primary" ], "version": "1.0", "note": "In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each 'omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.", "metadata": { "title": "Planet Microbe: A platform for marine microbiology to discover and analyze interconnected 'omics and environmental data'", "abstract": "In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and ongoing oceanographic sequencing efforts. In Planet Microbe, each 'omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets. 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BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.", "date": "2019-12-01T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Andrio P." }, { "name": "Hospital A." }, { "name": "Conejero J." }, { "name": "Jorda L." }, { "name": "Del Pino M." }, { "name": "Codo L." }, { "name": "Soiland-Reyes S." }, { "name": "Goble C." }, { "name": "Lezzi D." }, { "name": "Badia R.M." }, { "name": "Orozco M." }, { "name": "Gelpi J.L." } ], "journal": "Scientific Data" } }, { "doi": "10.1093/bioinformatics/btt324", "pmid": "23740746", "pmcid": null, "type": [ "Other" ], "version": null, "note": "GOdMD method", "metadata": { "title": "Exploration of conformational transition pathways from coarse-grained simulations", "abstract": "Motivation: A new algorithm to trace conformational transitions in proteins is presented. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics. The method, which shows an unprecedented computational efficiency, is able to trace a wide range of known experimental transitions. Contrary to simpler methods our strategy does not introduce distortions in the chemical structure of the protein and is able to reproduce well complex non-linear conformational transitions. The method, called GOdMD, can easily introduce additional restraints to the transition (presence of ligand, known intermediate, known maintained contacts, ...) and is freely distributed to the community through the Spanish National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD).Availability: Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.Contact: or modesto@mmb.pcb.ub.esSupplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. 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