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Our comprehensive and unique resource of all associations (https://helixomics.isglobal.org/) will serve to guide future investigation into the biological imprints of the early life exposome.", "date": "2022-12-01T00:00:00Z", "citationCount": 81, "authors": [ { "name": "Maitre L." }, { "name": "Bustamante M." }, { "name": "Hernandez-Ferrer C." }, { "name": "Thiel D." }, { "name": "Lau C.-H.E." }, { "name": "Siskos A.P." }, { "name": "Vives-Usano M." }, { "name": "Ruiz-Arenas C." }, { "name": "Pelegri-Siso D." }, { "name": "Robinson O." }, { "name": "Mason D." }, { "name": "Wright J." }, { "name": "Cadiou S." }, { "name": "Slama R." }, { "name": "Heude B." }, { "name": "Casas M." }, { "name": "Sunyer J." }, { "name": "Papadopoulou E.Z." }, { "name": "Gutzkow K.B." }, { "name": "Andrusaityte S." }, { "name": "Grazuleviciene R." }, { "name": "Vafeiadi M." }, { "name": "Chatzi L." }, { "name": "Sakhi A.K." }, { "name": "Thomsen C." }, { "name": "Tamayo I." }, { "name": "Nieuwenhuijsen M." }, { "name": "Urquiza J." }, { "name": "Borras E." }, { "name": "Sabido E." }, { "name": "Quintela I." }, { "name": "Carracedo A." }, { "name": "Estivill X." }, { "name": "Coen M." }, { "name": "Gonzalez J.R." }, { "name": "Keun H.C." }, { "name": "Vrijheid M." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@isglobal.org", "url": "http://www.carleshf.com", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Juan R Gonzalez", "email": "juanr.gonzalez@isglobal.org", "url": "https://brge.isglobal.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "chernan3", "additionDate": "2018-07-25T15:26:58Z", "lastUpdate": "2025-10-01T09:07:32.893505Z", "editPermission": { "type": "group", "authors": [ "brgelab", "sergitobara", "chernan3", "rodney" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SHARK.webservice", "description": "SHARK-Web is the webserver implementation of the SHARK-dive: a homology classifier trained to detect remote evolutionary homology and functional analogy for intrinsically disordered regions (IDRs) and other difficult-to-align protein regions. 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RNA secondary structure: the hairpin loop of the miRNA with bases.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_3500", "term": "Zoology" }, { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC0-1.0", "collectionID": [ "UiO tools", "ELIXIR-NO", "ELIXIR-Norway" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [], "link": [ { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://www.mirgenedb.org/download", "type": "Biological data", "note": "Sequence downloads for 75 species", "version": "3.0" } ], "documentation": [ { "url": "https://www.mirgenedb.org/information", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkab1101", "pmid": "34850127", "pmcid": "PMC8728216", "type": [ "Primary" ], "version": "2.1", "note": null, "metadata": { "title": "MirGeneDB 2.1: Toward a complete sampling of all major animal phyla", "abstract": "We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.", "date": "2022-01-07T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Fromm B." }, { "name": "Hoye E." }, { "name": "Domanska D." }, { "name": "Zhong X." }, { "name": "Aparicio-Puerta E." }, { "name": "Ovchinnikov V." }, { "name": "Umu S.U." }, { "name": "Chabot P.J." }, { "name": "Kang W." }, { "name": "Aslanzadeh M." }, { "name": "Tarbier M." }, { "name": "Marmol-Sanchez E." }, { "name": "Urgese G." }, { "name": "Johansen M." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Friedlander M.R." }, { "name": "Peterson K.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz885", "pmid": "31598695", "pmcid": "PMC6943042", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "MirGeneDB 2.0: The metazoan microRNA complement", "abstract": "Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database-MirGeneDB-to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.", "date": "2020-01-01T00:00:00Z", "citationCount": 178, "authors": [ { "name": "Fromm B." }, { "name": "Domanska D." }, { "name": "Hoye E." }, { "name": "Ovchinnikov V." }, { "name": "Kang W." }, { "name": "Aparicio-Puerta E." }, { "name": "Johansen M." }, { "name": "Flatmark K." }, { "name": "Mathelier A." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Friedlander M.R." }, { "name": "Peterson K.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1146/annurev-genet-120213-092023", "pmid": "26473382", "pmcid": "PMC4743252", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome", "abstract": "Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database-MirGeneDB (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.", "date": "2015-11-23T00:00:00Z", "citationCount": 435, "authors": [ { "name": "Fromm B." }, { "name": "Billipp T." }, { "name": "Peck L.E." }, { "name": "Johansen M." }, { "name": "Tarver J.E." }, { "name": "King B.L." }, { "name": "Newcomb J.M." }, { "name": "Sempere L.F." }, { "name": "Flatmark K." }, { "name": "Hovig E." }, { "name": "Peterson K.J." } ], "journal": "Annual Review of Genetics" } }, { "doi": "10.1093/nar/gkae1094", "pmid": "39673268", "pmcid": "PMC11701709", "type": [ "Primary" ], "version": "3.0", "note": null, "metadata": { "title": "MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models", "abstract": "We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB's phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.", "date": "2025-01-06T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Clarke A.W." }, { "name": "Hoye E." }, { "name": "Hembrom A.A." }, { "name": "Paynter V.M." }, { "name": "Vinther J." }, { "name": "Wyrozemski L." }, { "name": "Biryukova I." }, { "name": "Formaggioni A." }, { "name": "Ovchinnikov V." }, { "name": "Herlyn H." }, { "name": "Pierce A." }, { "name": "Wu C." }, { "name": "Aslanzadeh M." }, { "name": "Cheneby J." }, { "name": "Martinez P." }, { "name": "Friedlander M.R." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Umu S.U." }, { "name": "Johansen M." }, { "name": "Peterson K.J." }, { "name": "Fromm B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Bastian Fromm", "email": "BastianFromm@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-0352-3037", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Kevin J. Peterson", "email": "kevin.j.peterson@dartmouth.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "University of Oslo", "email": null, "url": "https://www.uio.no/english/index.html", "orcidid": null, "gridid": "grid.5510.1", "rorid": "01xtthb56", "fundrefid": "10.13039/501100005366", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "UiO", "additionDate": "2016-02-09T13:19:44Z", "lastUpdate": "2025-07-05T22:33:30.082420Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "purge_dups", "description": "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences", "homepage": "https://github.com/dfguan/purge_dups", "biotoolsID": "purge_dups", "biotoolsCURIE": "biotools:purge_dups", "version": [ "v.1.2.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "C" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/dfguan/purge_dups", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/dfguan/purge_dups/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/729962", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Dengfeng Guan", "email": null, "url": "https://www.chatlink.com.cn", "orcidid": "https://orcid.org/0000-0002-6376-3940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T18:08:10Z", "lastUpdate": "2025-06-30T15:34:51.626796Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Compleasm", "description": "Compleasm: a faster and more accurate reimplementation of BUSCO.\nIt provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.", "homepage": "https://github.com/huangnengCSU/compleasm", "biotoolsID": "compleasm", "biotoolsCURIE": "biotools:compleasm", "version": [ "v.0.2.5" ], "otherID": [], "relation": [ { "biotoolsID": "busco", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": "Runs compleasm using the BUSCO set corresponding to the lineage given.", "cmd": "compleasm run -l \"$lineage\" -a assembly.fa -o output_prefix" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/huangnengCSU/compleasm", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/huangnengCSU/compleasm/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://busco.ezlab.org/list_of_lineages.html", "type": [ "Other" ], "note": "List of accepted lineages (taxonomic groups with curated BUSCO sets)" } ], "download": [], "documentation": [ { "url": "https://github.com/huangnengCSU/compleasm/blob/0.2.6/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad595", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "compleasm: a faster and more accurate reimplementation of BUSCO", "abstract": "Motivation: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. Results: Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO's 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13.", "date": "2023-10-01T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Huang N." }, { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Neng Huang", "email": "neng@ds.dfci.harvard.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-7187-0749", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "rlibouban", "additionDate": "2024-03-18T14:51:49.667412Z", "lastUpdate": "2025-06-30T15:30:41.266812Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FANTASIAV2", "description": "FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeline for protein annotating via GO term transference using the embedding space. FANTASIA’s latest developments include additional protein language models and provide enhanced functionalities.", "homepage": "https://github.com/CBBIO/FANTASIA", "biotoolsID": "fantasiav2", "biotoolsCURIE": "biotools:fantasiav2", "version": [ "2.8.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3945", "term": "Molecular evolution" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_4010", "term": "Open science" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "SQL" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [ "3D-BioInfo", "Proteomics" ], "link": [ { "url": "https://github.com/CBBIO/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from latest version" }, { "url": "https://github.com/MetazoaPhylogenomicsLab/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from linitial version based on Bioembeddings implementation." }, { "url": "https://www.earthbiogenome.org/report-on-annotation-recommended-tools", "type": [ "Software catalogue" ], "note": "Recommended tool for the Earth Biogenome Project" } ], "download": [], "documentation": [ { "url": "https://fantasia.readthedocs.io/en/latest/", "type": [ "General" ], "note": "Full documetnation with user cases, benchmarking, and cluster implementations" } ], "publication": [ { "doi": "10.1093/nargab/lqae078", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Decoding functional proteome information in model organisms using protein language models", "abstract": "Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.", "date": "2024-09-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Barrios-Nunez I." }, { "name": "Martinez-Redondo G.I." }, { "name": "Medina-Burgos P." }, { "name": "Cases I." }, { "name": "Fernandez R." }, { "name": "Rojas A.M." } ], "journal": "NAR Genomics and Bioinformatics" } }, { "doi": "10.1101/2024.02.28.582465", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Francisco Miguel Pérez Canales", "email": "fmpercan@upo.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support", "Provider" ], "note": "Programmer" }, { "name": "Ana M Rojas Mendoza", "email": "a.rojas.m@csic.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Documentor", "Support" ], "note": "Scientific concept and functionalities" }, { "name": "Rosa Fernandez", "email": "rosa.fernandez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Documentor" ], "note": "Scientific concept and functionalities" }, { "name": "Francisco J. Ruiz Mota", "email": "fraruimot@alum.us.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Junior developer" }, { "name": "Gemma Martinez Redondo", "email": "gemma.martinez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": "Contributed as developer of the first version of FANTASIA V1" } ], "owner": "arojas", "additionDate": "2025-06-25T13:31:29.384393Z", "lastUpdate": "2025-06-25T14:34:50.629045Z", "editPermission": { "type": "group", "authors": [ "frapercan" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepSig", "description": "Prediction of secretory signal peptides in protein sequences", "homepage": "https://busca.biocomp.unibo.it/deepsig/", "biotoolsID": "deepsig", "biotoolsCURIE": "biotools:deepsig", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": "Source code", "note": null, "version": "1.2.5" }, { "url": "https://hub.docker.com/r/bolognabiocomp/deepsig", "type": "Container file", "note": null, "version": "1.2.5" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx818", "pmid": "29280997", "pmcid": "PMC5946842", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "DeepSig: Deep learning improves signal peptide detection in proteins", "abstract": "Motivation The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website.", "date": "2018-05-15T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://biocomp.unibo.it", "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": [ "Developer", "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": "http://biocomp.unibo.it", "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2018-05-28T14:50:09Z", "lastUpdate": "2025-06-19T11:55:09.017105Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "NanoPlot", "description": "NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences", "homepage": "https://github.com/wdecoster/NanoPlot", "biotoolsID": "nanoplot", "biotoolsCURIE": "biotools:nanoplot", "version": [ "v.1.42.0" ], "otherID": [], "relation": [ { "biotoolsID": "nanopack", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_2943", "term": "Box-Whisker plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" }, { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wdecoster/NanoPlot", "type": [ "Repository" ], "note": "Issue tracker and most up to date software version" }, { "url": "http://nanoplot.bioinf.be/", "type": [ "Service" ], "note": "Web service with more limited options compared to the command line tool" } ], "download": [ { "url": "https://anaconda.org/bioconda/nanoplot", "type": "Command-line specification", "note": null, "version": null }, { "url": "https://pypi.org/project/NanoPlot/", "type": "Command-line specification", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/wdecoster/NanoPlot", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty149", "pmid": "29547981", "pmcid": "PMC6061794", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "NanoPack: Visualizing and processing long-read sequencing data", "abstract": "Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.", "date": "2018-08-01T00:00:00Z", "citationCount": 1840, "authors": [ { "name": "De Coster W." }, { "name": "D'Hert S." }, { "name": "Schultz D.T." }, { "name": "Cruts M." }, { "name": "Van Broeckhoven C." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Wouter De Coster", "email": null, "url": "https://gigabaseorgigabyte.wordpress.com/", "orcidid": "https://orcid.org/0000-0002-5248-8197", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "wdecoster", "additionDate": "2021-07-06T20:27:27Z", "lastUpdate": "2025-06-18T12:31:48.762608Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SKM", "description": "Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.", "homepage": "https://skm.nib.si/", "biotoolsID": "skm", "biotoolsCURIE": "biotools:skm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "gomapman", "type": "uses" }, { "biotoolsID": "newt-ve", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3692", "term": "SBGN-ML" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "ELIXIR-SI", "Plant Systems Biology" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Slovenia" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://skm.nib.si/contact", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://skm.nib.si/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.xplc.2024.100920", "pmid": "38616489", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "metadata": { "title": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "abstract": "Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.", "date": "2024-06-10T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Bleker C." }, { "name": "Ramsak" }, { "name": "Bittner A." }, { "name": "Podpecan V." }, { "name": "Zagorscak M." }, { "name": "Wurzinger B." }, { "name": "Baebler" }, { "name": "Petek M." }, { "name": "Kriznik M." }, { "name": "van Dieren A." }, { "name": "Gruber J." }, { "name": "Afjehi-Sadat L." }, { "name": "Weckwerth W." }, { "name": "Zupanic A." }, { "name": "Teige M." }, { "name": "Vothknecht U.C." }, { "name": "Gruden K." } ], "journal": "Plant Communications" } } ], "credit": [ { "name": "National Institute of Biology, Department of Biotechnology and Systems Biology", "email": null, "url": "http://www.nib.si/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Carissa Bleker", "email": "carissarobyn.bleker@nib.si", "url": null, "orcidid": "https://orcid.org/0000-0003-1617-7145", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Kristina Gruden", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Živa Ramšak", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Vid Podpečan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "carissa", "additionDate": "2022-05-16T13:26:15.720803Z", "lastUpdate": "2025-06-18T12:10:26.465410Z", "editPermission": { "type": "group", "authors": [ "zagor" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Flye", "description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.", "homepage": "https://github.com/fenderglass/Flye", "biotoolsID": "Flye", "biotoolsCURIE": "biotools:Flye", "version": [ "2.9.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" }, { "uri": "http://edamontology.org/operation_3730", "term": "Cross-assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C++", "Python", "C" ], "license": "BSD-3-Clause", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/fenderglass/Flye/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/mikolmogorov/Flye", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1099/mgen.0.000294", "pmid": "31483244", "pmcid": "PMC6807382", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes", "abstract": "Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the longread assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.", "date": "2019-01-01T00:00:00Z", "citationCount": 166, "authors": [ { "name": "De Maio N." }, { "name": "Shaw L.P." }, { "name": "Hubbard A." }, { "name": "George S." }, { "name": "Sanderson N.D." }, { "name": "Swann J." }, { "name": "Wick R." }, { "name": "Oun M.A." }, { "name": "Stubberfield E." }, { "name": "Hoosdally S.J." }, { "name": "Crook D.W." }, { "name": "Peto T.E.A." }, { "name": "Sheppard A.E." }, { "name": "Bailey M.J." }, { "name": "Read D.S." }, { "name": "Anjum M.F." }, { "name": "Sarah Walker A." }, { "name": "Stoesser N." } ], "journal": "Microbial Genomics" } }, { "doi": "10.1038/s41587-019-0072-8", "pmid": "30936562", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Assembly of long, error-prone reads using repeat graphs", "abstract": "Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.", "date": "2019-05-01T00:00:00Z", "citationCount": 3077, "authors": [ { "name": "Kolmogorov M." }, { "name": "Yuan J." }, { "name": "Lin Y." }, { "name": "Pevzner P.A." } ], "journal": "Nature Biotechnology" } }, { "doi": "10.1038/s41592-020-00971-x", "pmid": "33020656", "pmcid": "PMC10699202", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "metaFlye: scalable long-read metagenome assembly using repeat graphs", "abstract": "Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. 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Disrupting this protein-protein interaction is an effective strategy for preventing infection and subsequent disease. Building on recent advances in computational tools for structural biology, we introduce Virus Inhibition via Peptide Engineering and Receptor Mimicry (VIPER), a novel approach for the automatic derivation and optimization of biomimetic decoy peptides that mimic binding sites of human proteins. VIPER leverages structural data from human-pathogen protein complexes, yielding peptides that can competitively inhibit viral entry by mimicking the natural receptor. We computationally validated VIPER using molecular dynamics simulations and showcased its applicability on three clinically relevant viruses, highlighting its potential to accelerate therapeutic development. 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Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: A RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.", "date": "2023-07-05T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Ribeiro-Filho H.V." }, { "name": "Pereira J.G.C." }, { "name": "Lopes-De-Oliveira P.S." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1021/acs.jcim.3c00328", "pmid": "37129917", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Cavity Characterization in Supramolecular Cages", "abstract": "Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.", "date": "2023-06-26T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Alves L.F.G." }, { "name": "Bourissou D." }, { "name": "Lopes-De-Oliveira P.S." }, { "name": "Szaloki G." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "João V. S. Guerra", "email": "joao.guerra@lnbio.cnpem.br", "url": "https://github.com/jvsguerra", "orcidid": "https://orcid.org/0000-0002-6800-4425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Helder V. Ribeiro-Filho", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "José G. C. 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