{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T20:01:27Z","timestamp":1762113687235,"version":"3.37.3"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,1,22]],"date-time":"2018-01-22T00:00:00Z","timestamp":1516579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Netherlands Organization for Scientific Research"},{"DOI":"10.13039\/501100003246","name":"NWO","doi-asserted-by":"publisher","award":["700.56.422"],"award-info":[{"award-number":["700.56.422"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Polypeptide sequence length is the single dominant factor hampering the effectiveness of currently available software tools for de novo calculation of amino acid-specific protonation constants in disordered polypeptides.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed pepKalc, a robust simulation software for the comprehensive evaluation of protein electrostatics in unfolded states. Our software completely removes the limitations of the previously reported Monte-Carlo approaches in the computation of protein electrostatics by using a hybrid approach that effectively combines exact and mean-field calculations to rapidly obtain accurate results. Paired with a modern architecture GPU, pepKalc is capable of evaluating protonation behavior for an arbitrary-size polypeptide in a sub-second time regime.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/protein-nmr.org and https:\/\/github.com\/PeptoneInc\/pepkalc<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty033","type":"journal-article","created":{"date-parts":[[2018,1,19]],"date-time":"2018-01-19T20:15:37Z","timestamp":1516392937000},"page":"2053-2060","source":"Crossref","is-referenced-by-count":12,"title":["pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0829-0615","authenticated-orcid":false,"given":"Kamil","family":"Tamiola","sequence":"first","affiliation":[{"name":"Peptone \u2013 The Protein Intelligence Company, Amsterdam, The Netherlands"},{"name":"Department of Molecular Dynamics, GBB, University of Groningen, Groningen, The Netherlands"}]},{"given":"Ruud M","family":"Scheek","sequence":"additional","affiliation":[{"name":"Department of Molecular Dynamics, GBB, University of Groningen, Groningen, The Netherlands"}]},{"given":"Pieter","family":"van der Meulen","sequence":"additional","affiliation":[{"name":"Department of Molecular Dynamics, GBB, University of Groningen, Groningen, The Netherlands"}]},{"given":"Frans A A","family":"Mulder","sequence":"additional","affiliation":[{"name":"Department of Molecular Dynamics, GBB, University of Groningen, Groningen, The Netherlands"},{"name":"Department of Chemistry and Interdisciplinary Nanoscience Center iNANO, Aarhus University, Aarhus, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2018,1,22]]},"reference":[{"key":"2023012713393475800_bty033-B1","doi-asserted-by":"crossref","first-page":"3260","DOI":"10.1002\/prot.23189","article-title":"Progress in the prediction of pKa values in proteins","volume":"79","author":"Alexov","year":"2011","journal-title":"Proteins Struct. 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