{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,19]],"date-time":"2026-04-19T15:44:32Z","timestamp":1776613472344,"version":"3.51.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":201,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein\u2013surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies.<\/jats:p>\n               <jats:p>Availability and Implementation: ProtPOS is freely available for academic and non-profit uses at http:\/\/cbbio.cis.umac.mo\/software\/protpos<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: shirleysiu@umac.mo<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw182","type":"journal-article","created":{"date-parts":[[2016,4,12]],"date-time":"2016-04-12T01:13:10Z","timestamp":1460423590000},"page":"2537-2538","source":"Crossref","is-referenced-by-count":8,"title":["ProtPOS: a python package for the prediction of protein preferred orientation on a surface"],"prefix":"10.1093","volume":"32","author":[{"given":"Jimmy C. F.","family":"Ngai","sequence":"first","affiliation":[{"name":"1 Department of Computer and Information Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pui-In","family":"Mak","sequence":"additional","affiliation":[{"name":"2 State-Key Laboratory of Analog and Mixed-Signal VLSI, Faculty of Science and Technology, University of Macau (UM), Avenida da Universidade, Taipa, Macau, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shirley W. I.","family":"Siu","sequence":"additional","affiliation":[{"name":"1 Department of Computer and Information Science"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,4,10]]},"reference":[{"key":"2023020112524286300_btw182-B1","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.colsurfb.2008.08.017","article-title":"Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation","volume":"67","author":"Hsu","year":"2008","journal-title":"Colloids Surf. B Biointerf"},{"key":"2023020112524286300_btw182-B2","author":"Kennedy","year":"1995"},{"key":"2023020112524286300_btw182-B3","doi-asserted-by":"crossref","first-page":"13713","DOI":"10.1021\/ja074602v","article-title":"Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite","volume":"129","author":"Makrodimitris","year":"2007","journal-title":"J. Am. Chem. Soc"},{"key":"2023020112524286300_btw182-B4","author":"Ngai","year":"2015"},{"key":"2023020112524286300_btw182-B5","doi-asserted-by":"crossref","first-page":"5616","DOI":"10.1021\/la046932o","article-title":"Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation","volume":"21","author":"Sun","year":"2005","journal-title":"Langmuir"},{"key":"2023020112524286300_btw182-B6","doi-asserted-by":"crossref","first-page":"10189","DOI":"10.1021\/jp304057e","article-title":"Molecular dynamics simulation of lysozyme adsorption\/desorption on hydrophobic surfaces","volume":"116","author":"Wei","year":"2012","journal-title":"J. Phys. Chem. B"},{"key":"2023020112524286300_btw182-B7","doi-asserted-by":"crossref","first-page":"065101","DOI":"10.1063\/1.3305244","article-title":"Parallel tempering monte carlo simulations of lysozyme orientation on charged surfaces","volume":"132","author":"Xie","year":"2010","journal-title":"J. Chem. Phys"},{"key":"2023020112524286300_btw182-B8","doi-asserted-by":"crossref","first-page":"8931","DOI":"10.1021\/la036345n","article-title":"Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers","volume":"20","author":"Zheng","year":"2004","journal-title":"Langmuir"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/16\/2537\/49019981\/bioinformatics_32_16_2537.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/16\/2537\/49019981\/bioinformatics_32_16_2537.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:30:46Z","timestamp":1675290646000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/16\/2537\/1743326"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,10]]},"references-count":8,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2016,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw182","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,8,15]]},"published":{"date-parts":[[2016,4,10]]}}}