{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T15:52:33Z","timestamp":1765295553088,"version":"3.41.2"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T00:00:00Z","timestamp":1747267200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Molecular dynamics (MD) simulations provide critical insights into biomolecular processes but they generate complex high-dimensional data that are often difficult to interpret directly. Dimensionality reduction methods like principal component analysis, time-lagged independent component analysis, and self-organizing maps (SOMs) have helped in extracting essential information on functional dynamics. However, there is a growing need for a user-friendly and flexible framework for SOM-based analyses of MD simulations. Such a framework should offer adaptable workflows, customizable options, and direct integration with a widely adopted analysis software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We designed and developed SOMMD, an R package to streamline MD analysis workflows. SOMMD facilitates the interpretation of atomistic trajectories through SOMs, providing tools for each stage of the workflow, from importing a wide range of MD trajectories data types to generating enhanced visualizations. The package also includes three example projects that demonstrate how SOM can be applied in real-world scenarios, including cluster analysis, pathways mapping and transition networks reconstruction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SOMMD is available on CRAN (https:\/\/CRAN.R-project.org\/package=SOMMD) and on GitHub (https:\/\/github.com\/alepandini\/SOMMD).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf308","type":"journal-article","created":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T15:04:01Z","timestamp":1747321441000},"source":"Crossref","is-referenced-by-count":1,"title":["SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0812-6834","authenticated-orcid":false,"given":"Stefano","family":"Motta","sequence":"first","affiliation":[{"name":"Department of Earth and Environmental Sciences, University of Milano-Bicocca , Milan, 20126,","place":["Italy"]}]},{"given":"Lara","family":"Callea","sequence":"additional","affiliation":[{"name":"Department of Earth and Environmental Sciences, University of Milano-Bicocca , Milan, 20126,","place":["Italy"]}]},{"given":"Shaziya Ismail","family":"Mulla","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Brunel University of London , Uxbridge UB8 3PH,","place":["United Kingdom"]}]},{"given":"Hamid","family":"Davoudkhani","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Brunel University of London , Uxbridge UB8 3PH,","place":["United Kingdom"]}]},{"given":"Laura","family":"Bonati","sequence":"additional","affiliation":[{"name":"Department of Earth and Environmental Sciences, University of Milano-Bicocca , Milan, 20126,","place":["Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4158-233X","authenticated-orcid":false,"given":"Alessandro","family":"Pandini","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Brunel University of London , Uxbridge UB8 3PH,","place":["United Kingdom"]},{"name":"The Thomas Young Centre for Theory and Simulation of Materials , London SW7 2AZ,","place":["United Kingdom"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,15]]},"reference":[{"journal-title":"aweSOM: Interactive Self.Organizing Maps","author":"Boelaert","key":"2025070408275129400_btaf308-B24"},{"key":"2025070408275129400_btaf308-B1","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.1093\/bioinformatics\/btu849","article-title":"An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps","volume":"31","author":"Bouvier","year":"2015","journal-title":"Bioinformatics"},{"key":"2025070408275129400_btaf308-B2","doi-asserted-by":"publisher","first-page":"3841","DOI":"10.1021\/acs.jctc.1c00114","article-title":"Metadynamics-based approaches for modeling the hypoxia-inducible factor 2\u03b1 ligand binding process","volume":"17","author":"Callea","year":"2021","journal-title":"J Chem Theory Comput"},{"key":"2025070408275129400_btaf308-B3","doi-asserted-by":"publisher","first-page":"135102","DOI":"10.1063\/5.0225183","article-title":"Self-organizing maps of unbiased ligand\u2013target binding pathways and kinetics","volume":"161","author":"Callea","year":"2024","journal-title":"J Chem Phys"},{"key":"2025070408275129400_btaf308-B4","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-biophys-042910-155245","article-title":"Biomolecular simulation: a computational microscope for molecular biology","volume":"41","author":"Dror","year":"2012","journal-title":"Annu Rev Biophys"},{"key":"2025070408275129400_btaf308-B5","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/1471-2105-12-158","article-title":"Conformational and functional analysis of molecular dynamics trajectories by self-organising maps","volume":"12","author":"Fraccalvieri","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2025070408275129400_btaf308-B6","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","article-title":"Bio3d: an R package for the comparative analysis of protein structures","volume":"22","author":"Grant","year":"2006","journal-title":"Bioinformatics"},{"journal-title":"popsom7: A Fast, User-Friendly Implementation of Self-Organizing Maps (SOMs).","author":"Hamel","key":"2025070408275129400_btaf308-B25"},{"key":"2025070408275129400_btaf308-B7","doi-asserted-by":"publisher","first-page":"7934","DOI":"10.1021\/acs.jpcb.2c04770","article-title":"Insight into the initial stages of the folding process in onconase revealed by UNRES","volume":"126","author":"Hendrix","year":"2022","journal-title":"J Phys Chem B"},{"key":"2025070408275129400_btaf308-B8","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1016\/j.neuron.2018.08.011","article-title":"Molecular dynamics simulation for all","volume":"99","author":"Hollingsworth","year":"2018","journal-title":"Neuron"},{"key":"2025070408275129400_btaf308-B9","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1109\/5.58325","article-title":"The self-organizing map","volume":"78","author":"Kohonen","year":"1990","journal-title":"Proc IEEE"},{"key":"2025070408275129400_btaf308-B10","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/j.neunet.2012.09.018","article-title":"Essentials of the self-organizing map","volume":"37","author":"Kohonen","year":"2013","journal-title":"Neural Netw"},{"year":"2022","author":"Maechler","key":"2025070408275129400_btaf308-B11"},{"key":"2025070408275129400_btaf308-B12","doi-asserted-by":"publisher","first-page":"3634","DOI":"10.1103\/PhysRevLett.72.3634","article-title":"Separation of a mixture of independent signals using time delayed correlations","volume":"72","author":"Molgedey","year":"1994","journal-title":"Phys Rev Lett"},{"key":"2025070408275129400_btaf308-B13","doi-asserted-by":"publisher","first-page":"1957","DOI":"10.1021\/ACS.JCTC.1C01163","article-title":"PathDetect-SOM: a neural network approach for the identification of pathways in ligand binding simulations","volume":"18","author":"Motta","year":"2022","journal-title":"J Chem Theory Comput"},{"key":"2025070408275129400_btaf308-B14","doi-asserted-by":"publisher","first-page":"2080","DOI":"10.1021\/acs.jctc.0c01308","article-title":"Re-construction of ARNT PAS-B unfolding pathways by steered molecular dynamics and artificial neural networks","volume":"17","author":"Motta","year":"2021","journal-title":"J Chem Theory Comput"},{"key":"2025070408275129400_btaf308-B15","doi-asserted-by":"publisher","first-page":"7909","DOI":"10.1039\/D3NR00397C","article-title":"Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles","volume":"15","author":"Motta","year":"2023","journal-title":"Nanoscale"},{"key":"2025070408275129400_btaf308-B16","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1137\/110858616","article-title":"A variational approach to modeling slow processes in stochastic dynamical systems","volume":"11","author":"No\u00e9","year":"2013","journal-title":"Multiscale Model Simul"},{"key":"2025070408275129400_btaf308-B17","doi-asserted-by":"publisher","first-page":"7729","DOI":"10.1021\/acs.jcim.3c01130","article-title":"Attempting well-tempered funnel metadynamics simulations for the evaluation of the binding kinetics of methionine aminopeptidase-II inhibitors","volume":"63","author":"Rubina","year":"2023","journal-title":"J Chem Inf Model"},{"key":"2025070408275129400_btaf308-B18","doi-asserted-by":"publisher","first-page":"2312","DOI":"10.1021\/ct700119m","article-title":"Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clus-tering algorithms","volume":"3","author":"Shao","year":"2007","journal-title":"J Chem Theory Comput"},{"key":"2025070408275129400_btaf308-B19","doi-asserted-by":"publisher","first-page":"5182","DOI":"10.1021\/acs.jcim.3c00376","article-title":"Temperature accelerated sliced sampling to probe ligand dissociation from protein","volume":"63","author":"Tripathi","year":"2023","journal-title":"J Chem Inf Model"},{"key":"2025070408275129400_btaf308-B20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v021.i05","article-title":"Self- and super-organizing maps in R: the kohonen package","volume":"21","author":"Wehrens","year":"2007","journal-title":"J Stat Soft"},{"key":"2025070408275129400_btaf308-B21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v087.i07","article-title":"Flexible Self-Organizing maps in kohonen 3.0","volume":"87","author":"Wehrens","year":"2018","journal-title":"J Stat Soft"},{"key":"2025070408275129400_btaf308-B22","doi-asserted-by":"publisher","first-page":"20819","DOI":"10.1021\/acsomega.3c09433","article-title":"Insights into the dis-sociation process and binding pattern of the BRCT7\/8-PHF8 complex","volume":"9","author":"Yuan","year":"2024","journal-title":"ACS Omega"},{"key":"2025070408275129400_btaf308-B23","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1007\/s00894-024-05946-9","article-title":"Unveiling dissociation mechanisms and binding patterns in the UHRF1-DPPA3 complex via multi-replica molecular dynamics simulations","volume":"30","author":"Yuan","year":"2024","journal-title":"J Mol Model"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf308\/63196707\/btaf308.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/6\/btaf308\/63196707\/btaf308.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/6\/btaf308\/63196707\/btaf308.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T12:27:56Z","timestamp":1751632076000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf308\/8132949"}},"subtitle":[],"editor":[{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,5,15]]},"references-count":25,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,6,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf308","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,6]]},"published":{"date-parts":[[2025,5,15]]},"article-number":"btaf308"}}