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Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. 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Transitions", "description": "This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks (biobb).", "homepage": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd", "biotoolsID": "bioexcel_building_blocks_tutorials_protein_conformational_transitions", "biotoolsCURIE": "biotools:bioexcel_building_blocks_tutorials_protein_conformational_transitions", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "biobb", "type": "uses" }, { "biotoolsID": "godmd", "type": "uses" }, { "biotoolsID": "water", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" }, { "uri": 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"Molecular modelling" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "BioExcel" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "Spain", "UK" ], "elixirCommunity": [], "link": [ { "url": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd", "type": [ "Other" ], "note": "Tutorial in HTML" }, { "url": "https://biobb-wf-godmd.readthedocs.io/en/latest/index.html", "type": [ "Other" ], "note": "Tutorial in Read the Docs" }, { "url": "https://github.com/bioexcel/biobb_wf_godmd", "type": [ "Repository" ], "note": "Source Code in GitHub" } ], "download": [ { "url": "https://github.com/bioexcel/biobb_wf_godmd", "type": "Source code", "note": "Source Code in GitHub", "version": "1.0" }, { "url": "https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_godmd/main?filepath=biobb_wf_godmd%2Fnotebooks%2Fbiobb_wf_godmd.ipynb", "type": "VM image", "note": "BioExcel Binder", "version": null } ], "documentation": [ { "url": "https://biobb-wf-godmd.readthedocs.io/en/latest/index.html", "type": [ "Other" ], "note": "Documentation in Read the Docs" } ], "publication": [ { "doi": "10.1038/s41597-019-0177-4", "pmid": "31506435", "pmcid": "PMC6736963", "type": [ "Other" ], "version": null, "note": "BioExcel Building Blocks (BioBB)", "metadata": { "title": "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows", "abstract": "In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. 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. Published by Oxford University Press.", "date": "2013-08-15T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Sfriso P." }, { "name": "Hospital A." }, { "name": "Emperador A." }, { "name": "Orozco M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Adam Hospital Gasch", "email": "adam.hospital@irbbarcelona.org", "url": "https://www.irbbarcelona.org/en/research/adam-hospital", "orcidid": "https://orcid.org/0000-0002-8291-8071", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Genís Bayarri", "email": "genis.bayarri@irbbarcelona.org", "url": "https://www.irbbarcelona.org/es/research/genis-bayarri", "orcidid": "https://orcid.org/0000-0003-0513-0288", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer", "Maintainer" ], "note": null }, { "name": "BioExcel CoE", "email": null, "url": "https://bioexcel.eu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "adam.hospital@irbbarcelona.org", "additionDate": "2023-08-31T07:04:02.274853Z", "lastUpdate": "2023-08-31T07:33:54.784700Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioExcel Building Blocks tutorials: Molecular Interaction Potentials", "description": "This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures step by step, using the BioExcel Building Blocks library (biobb)", "homepage": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmip", "biotoolsID": "bioexcel_building_blocks_tutorials_molecular_interaction_potentials", "biotoolsCURIE": 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"http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "BioExcel" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "Spain", "UK" ], "elixirCommunity": [], "link": [ { "url": "https://mmb.irbbarcelona.org/biobb/workflows#macromolecular-coarse-grained-flexibility", "type": [ "Other" ], "note": "Main web site (BioBB Workflows)" }, { "url": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexserv", "type": [ "Other" ], "note": "Tutorial in HTML" }, { "url": "https://biobb-wf-flexserv.readthedocs.io/en/latest/index.html", "type": [ "Other" ], "note": "Tutorial in Read The Docs" }, { "url": "https://github.com/bioexcel/biobb_wf_flexserv", "type": [ "Repository" ], "note": "Source Code in GitHub" } ], "download": [ { "url": "https://github.com/bioexcel/biobb_wf_flexserv", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_flexserv/main?filepath=biobb_wf_flexserv%2Fnotebooks%2Fbiobb_wf_flexserv.ipynb", "type": "VM image", "note": "BioExcel Binder", "version": "1.0" } ], "documentation": [ { "url": "https://biobb-wf-flexserv.readthedocs.io/en/latest/index.html", "type": [ "Other" ], "note": "Read The Docs workflow documentation" } ], "publication": [ { "doi": "10.1038/s41597-019-0177-4", "pmid": "31506435", "pmcid": "PMC6736963", "type": [ "Other" ], "version": null, "note": "BioExcel Building Blocks (BioBB)", "metadata": { "title": "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows", "abstract": "In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. 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" } } ], "credit": [ { "name": "Adam Hospital", "email": "adam.hospital@irbbarcelona.org", "url": "https://www.irbbarcelona.org/en/research/adam-hospital", "orcidid": "https://orcid.org/0000-0002-8291-8071", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Genís Bayarri", "email": "genis.bayarri@irbbarcelona.org", "url": "https://www.irbbarcelona.org/es/research/genis-bayarri", "orcidid": "https://orcid.org/0000-0003-0513-0288", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer", "Maintainer" ], "note": null }, { "name": "BioExcel CoE", "email": null, "url": "https://bioexcel.eu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "adam.hospital@irbbarcelona.org", "additionDate": "2023-08-29T10:55:17.540852Z", "lastUpdate": "2023-08-29T10:55:17.543854Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GERONIMO", "description": "GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.", "homepage": "https://github.com/amkilar/GERONIMO.git", "biotoolsID": "GERONIMO", "biotoolsCURIE": "biotools:GERONIMO", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "infernal", "type": "uses" } ], "function": [], "toolType": [ "Workflow", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Windows", "Linux" ], "language": [ "Python", "R", "Bash" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": 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Generic Format or MGF.", "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" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "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": [], "elixirCommunity": [], "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": 26, "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": 1, "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": [ "Provider" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": null, "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": null, "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "n.m.palmblad@lumc.nl", "additionDate": "2016-04-15T11:52:42Z", "lastUpdate": "2023-07-26T15:16:22.382984Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Kojak", "description": "A database search algorithm for solving cross-linked peptide mass spectra.", "homepage": "https://kojak-ms.systemsbiology.net/", "biotoolsID": "kojak", "biotoolsCURIE": "biotools:kojak", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [ "C++" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Proteomics" ], "link": [], "download": [ { "url": "https://kojak-ms.systemsbiology.net/download.html", "type": "Downloads page", "note": null, "version": "1.0 - 2.0.0" } ], "documentation": [ { "url": "https://kojak-ms.systemsbiology.net/docs/index.html", "type": [ "Quick start guide", "Installation instructions", "User manual" ], "note": null }, { "url": "https://kojak-ms.systemsbiology.net/param/index.html", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1021/pr501321h", "pmid": "25812159", "pmcid": "PMC4428575", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Kojak: Efficient analysis of chemically cross-linked protein complexes", "abstract": "Protein chemical cross-linking and mass spectrometry enable the analysis of protein-protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein-protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithms. The algorithm provided increased cross-link identifications over existing algorithms and, equally importantly, the results in a fraction of computational time. The Kojak algorithm is open-source, cross-platform, and freely available. This software provides both existing and new cross-linking researchers alike an effective way to derive additional cross-link identifications from new or existing data sets. For new users, it provides a simple analytical resource resulting in more cross-link identifications than other methods.", "date": "2015-05-01T00:00:00Z", "citationCount": 126, "authors": [ { "name": "Hoopmann M.R." }, { "name": "Zelter A." }, { "name": "Johnson R.S." }, { "name": "Riffle M." }, { "name": "Maccoss M.J." }, { "name": "Davis T.N." }, { "name": "Moritz R.L." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.2c00670", "pmid": "36629399", "pmcid": "PMC10234491", "type": [ "Primary" ], "version": "2.0.0", "note": null, "metadata": { "title": "Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline", "abstract": "Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between 15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of cross-links improve the sensitivity and accuracy of correct cross-link identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multiplatform.", "date": "2023-02-03T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Hoopmann M.R." }, { "name": "Shteynberg D.D." }, { "name": "Zelter A." }, { "name": "Riffle M." }, { "name": "Lyon A.S." }, { "name": "Agard D.A." }, { "name": "Luan Q." }, { "name": "Nolen B.J." }, { "name": "MacCoss M.J." }, { "name": "Davis T.N." }, { "name": "Moritz R.L." } ], "journal": "Journal of Proteome Research" } } ], "credit": [], "community": null, "owner": "mhoopmann", "additionDate": "2023-07-26T14:34:25.798022Z", "lastUpdate": "2023-07-26T14:48:27.327393Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SuchTree", "description": "A Python library for doing fast, thread-safe computations with phylogenetic trees.", "homepage": "https://github.com/ryneches/SuchTree", "biotoolsID": "suchtree", "biotoolsCURIE": "biotools:suchtree", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0557", "term": "Phylogenetic tree distances calculation" }, { "uri": "http://edamontology.org/operation_0551", "term": "Phylogenetic tree topology analysis" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3271", "term": "Gene tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [ { "uri": "http://edamontology.org/format_4003", "term": "NumPy format" } ] } ], "note": null, "cmd": "SuchTree.distances_by_name()" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ryneches/SuchTree", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ryneches/SuchTree/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/SuchTree/", "type": "Software package", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://github.com/ryneches/SuchTree#readme", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.21105/joss.00678", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "0.7", "note": null, "metadata": null } ], "credit": [ { "name": "Russell Y. Neches", "email": null, "url": "https://vort.org", "orcidid": "https://orcid.org/0000-0002-2055-8381", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Camille Scott", "email": null, "url": "http://www.camillescott.org/", "orcidid": "https://orcid.org/0000-0001-8822-8779", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "ryneches", "additionDate": "2023-07-03T10:51:19.368916Z", "lastUpdate": "2023-07-03T10:51:39.215013Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3D-BioInfo + BioExcel: Protein Conformational Ensembles Generation", "description": "This workflow illustrates the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb). Workflow included in the ELIXIR 3D-Bioinfo Implementation Study: Building on PDBe-KB to chart and characterize the conformation landscape of native proteins", "homepage": "https://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation", "biotoolsID": "3d-bioinfo_bioexcel_protein_conformational_ensembles_generation", "biotoolsCURIE": "biotools:3d-bioinfo_bioexcel_protein_conformational_ensembles_generation", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "biobb", "type": "uses" }, { "biotoolsID": "imod", "type": "uses" }, { "biotoolsID": "flexserv", "type": "uses" }, { "biotoolsID": "prody", "type": "uses" }, { "biotoolsID": "nglview", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" }, { "uri": "http://edamontology.org/operation_3890", "term": "Trajectory visualization" }, { "uri": "http://edamontology.org/operation_0250", "term": "Protein property calculation" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3870", "term": "Trajectory data" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3874", "term": "PCAzip" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3892", "term": "Biomolecular simulation" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "BioExcel", "3D-BioInfo", "3D-BioInfo-Protein-Complex" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Interoperability", "Tools" ], "elixirNode": [ "Spain", "Norway", "France", "Belgium", "EMBL", "Hungary", "Denmark" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation", "type": [ "Other" ], "note": "Main web site (BioBB workflows)" }, { "url": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexdyn", "type": [ "Other" ], "note": "Tutorial in HTML" }, { "url": "https://biobb-wf-flexdyn.readthedocs.io/en/latest/index.html", "type": [ "Other" ], "note": "Tutorial in Read The Docs" }, { "url": "https://github.com/bioexcel/biobb_wf_flexdyn", "type": [ "Repository" ], "note": "Source Code in GitHub" } ], "download": [ { "url": "https://github.com/bioexcel/biobb_wf_flexdyn", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_md_setup/master?filepath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb", "type": "VM image", "note": "BioExcel Binder", "version": "1.0" } ], "documentation": [ { "url": "https://biobb-wf-flexdyn.readthedocs.io/en/latest/?badge=latest", "type": [ "Other" ], "note": "Read The Docs Workflow Documentation" } ], "publication": [ { "doi": "10.1038/s41597-019-0177-4", "pmid": "31506435", "pmcid": "PMC6736963", "type": [ "Other" ], "version": null, "note": "BioExcel Building Blocks (BioBB)", "metadata": { "title": "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows", "abstract": "In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. 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": 28, "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": "10.12688/f1000research.20559.1", "pmid": "32566135", "pmcid": "PMC7284151", "type": [ "Other" ], "version": null, "note": "3D-BioInfo, ELIXIR Structural Community", "metadata": { "title": "A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)", "abstract": "Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.", "date": "2020-01-01T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Orengo C." }, { "name": "Velankar S." }, { "name": "Wodak S." }, { "name": "Zoete V." }, { "name": "Bonvin A.M.J.J." }, { "name": "Elofsson A." }, { "name": "Feenstra K.A." }, { "name": "Gerloff D.L." }, { "name": "Hamelryck T." }, { "name": "Hancock J.M." }, { "name": "Helmer-Citterich M." }, { "name": "Hospital A." }, { "name": "Orozco M." }, { "name": "Perrakis A." }, { "name": "Rarey M." }, { "name": "Soares C." }, { "name": "Sussman J.L." }, { "name": "Thornton J.M." }, { "name": "Tuffery P." }, { "name": "Tusnady G." }, { "name": "Wierenga R." }, { "name": "Salminen T." }, { "name": "Schneider B." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "Adam Hospital", "email": "adam.hospital@irbbarcelona.org", "url": "https://www.irbbarcelona.org/en/research/adam-hospital", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Genís Bayarri", "email": "genis.bayarri@irbbarcelona.org", "url": "https://www.irbbarcelona.org/en/research/genis-bayarri", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Maintainer" ], "note": null }, { "name": "3D-BioInfo", "email": "katharina.heil@elixir-europe.org", "url": "https://elixir-europe.org/communities/3d-bioinfo", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "adam.hospital@irbbarcelona.org", "additionDate": "2023-05-25T11:54:30.874289Z", "lastUpdate": "2023-05-25T11:54:30.877367Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "mirKit", "description": "miRkit is an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the tool is to provide an assessment of the samples’ quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, can perform the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and is specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology.", "homepage": "https://github.com/BiodataAnalysisGroup/miRkit", "biotoolsID": "mirkit", "biotoolsCURIE": "biotools:mirkit", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_3792", "term": "miRNA expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [ { "uri": "http://edamontology.org/format_1957", "term": "raw" }, { "uri": "http://edamontology.org/format_3999", "term": "R script" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BiodataAnalysisGroup/miRkit", "type": "Source code", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://github.com/BiodataAnalysisGroup/miRkit/blob/main/README.md", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Fotis Psomopoulos", "email": "fpsom@certh.gr", "url": null, "orcidid": "https://orcid.org/0000-0002-0222-4273", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "fpsom", "additionDate": "2021-09-20T06:49:28.552326Z", "lastUpdate": "2022-12-01T22:34:37.796805Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }