{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T16:48:34Z","timestamp":1772902114354,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T00:00:00Z","timestamp":1730851200000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Academic Infrastructure for Supercomputing in Sweden"},{"name":"Swedish National Infrastructure for Computing","award":["NGFOP2201"],"award-info":[{"award-number":["NGFOP2201"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Memprot.GPCR-ModSim leverages our previous web-based protocol, which was limited to class-A G protein-coupled receptors, to become the first one-stop web server for the modelling and simulation of any membrane protein system. Motivated by the exponential growth of experimental structures and the breakthrough of deep-learning-based structural modelling, the server accepts as input either a membrane-protein sequence, in which case it reports the associated AlphaFold model, or a 3D (experimental, modelled) structure, including quaternary complexes with associated proteins and\/or ligands of any kind. In both cases, the molecular dynamics (MD) protocol produces a membrane-embedded, solvated, and equilibrated system, ready to be used as a starting point for further MD simulations, including ligand-binding free energy calculations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Memprot.GPCR-ModSim web server is publicly available at https:\/\/memprot.gpcr-modsim.org\/. The standalone modules for 3D modelling (PyModSim) or membrane embedding and MD equilibration (PyMemDyn) are available under CC BY-NC 4.0 license terms at the GitHub repository https:\/\/github.com\/GPCR-ModSim\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae662","type":"journal-article","created":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T19:49:42Z","timestamp":1730922582000},"source":"Crossref","is-referenced-by-count":3,"title":["Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5661-1157","authenticated-orcid":false,"given":"Remco L","family":"van den Broek","sequence":"first","affiliation":[{"name":"Department of Cell and Molecular Biology, Uppsala University , BMC - Box 596 , Uppsala, SE 751 24,","place":["Sweden"]},{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , Leiden 2333 CC,","place":["The Netherlands"]}]},{"given":"Xabier","family":"Bello","sequence":"additional","affiliation":[{"name":"Institute of Forensic Sciences, Faculty of Medicine, University of Santiago de Compostela , Hospital Cl\u00ednico Universitario de Santiago de Compostela (SERGAS) Santiago de Compostela, Galicia, 15706,","place":["Spain"]}]},{"given":"Rebecca V","family":"K\u00fcpper","sequence":"additional","affiliation":[{"name":"Department of Cell and Molecular Biology, Uppsala University , BMC - Box 596 , Uppsala, SE 751 24,","place":["Sweden"]}]},{"given":"Gerard J P","family":"van Westen","sequence":"additional","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , Leiden 2333 CC,","place":["The Netherlands"]}]},{"given":"Willem","family":"Jespers","sequence":"additional","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University , Leiden 2333 CC,","place":["The Netherlands"]},{"name":"MOD4SIM Pharma AB , Box 2022 , Uppsala, SE 750 02,","place":["Sweden"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0459-3491","authenticated-orcid":false,"given":"Hugo","family":"Guti\u00e9rrez-de-Ter\u00e1n","sequence":"additional","affiliation":[{"name":"Department of Cell and Molecular Biology, Uppsala University , BMC - Box 596 , Uppsala, SE 751 24,","place":["Sweden"]},{"name":"MOD4SIM Pharma AB , Box 2022 , Uppsala, SE 750 02,","place":["Sweden"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,6]]},"reference":[{"key":"2024112022353389900_btae662-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through Multi-Level parallelism from laptops to supercomputers","volume":"1-2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2024112022353389900_btae662-B2","doi-asserted-by":"crossref","first-page":"2002","DOI":"10.1016\/S0006-3495(97)78845-3","article-title":"Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature","volume":"72","author":"Berger","year":"1997","journal-title":"Biophys J"},{"key":"2024112022353389900_btae662-B3","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.sbi.2011.06.007","article-title":"Lipidic cubic phase technologies for membrane protein structural studies","volume":"21","author":"Cherezov","year":"2011","journal-title":"Curr Opin Struct Biol"},{"key":"2024112022353389900_btae662-B4","doi-asserted-by":"crossref","first-page":"W331","DOI":"10.1093\/nar\/gkx312","article-title":"LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands","volume":"45","author":"Dodda","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024112022353389900_btae662-B5","doi-asserted-by":"crossref","first-page":"W455","DOI":"10.1093\/nar\/gkw403","article-title":"GPCR-ModSim: a comprehensive web based solution for modeling G-Protein coupled receptors","volume":"44","author":"Esguerra","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024112022353389900_btae662-B6","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.1124\/mol.63.6.1256","article-title":"The G-protein-coupled receptors in the human genome form five main families. 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