{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T04:53:51Z","timestamp":1793940831781,"version":"4.8.0"},"reference-count":80,"publisher":"Informa UK Limited","issue":"19","content-domain":{"domain":["www.tandfonline.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biomolecular Structure and Dynamics"],"published-print":{"date-parts":[[2023,11,24]]},"DOI":"10.1080\/07391102.2022.2153920","type":"journal-article","created":{"date-parts":[[2022,12,8]],"date-time":"2022-12-08T01:46:08Z","timestamp":1670463968000},"page":"10190-10201","update-policy":"https:\/\/doi.org\/10.1080\/tandf_crossmark_01","source":"Crossref","is-referenced-by-count":13,"title":["Computational study to investigate\n            <i>Proteus mirabilis<\/i>\n            proteomes for multi-epitope vaccine construct design"],"prefix":"10.1080","volume":"41","author":[{"given":"Asad","family":"Ullah","sequence":"first","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saif","family":"Ullah Khan","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahboob Ul","family":"Haq","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Abasyn University, Peshawar, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajjad","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Irfan","sequence":"additional","affiliation":[{"name":"Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Asif","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyad Tariq","family":"Muhseen","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon, Iraq"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monerh Saleh","family":"Alkeraidees","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khaled S.","family":"Allemailem","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faris","family":"Alrumaihi","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1491-6402","authenticated-orcid":false,"given":"Ahmad","family":"Almatroudi","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"301","published-online":{"date-parts":[[2022,12,7]]},"reference":[{"key":"e_1_3_3_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejps.2019.02.023"},{"key":"e_1_3_3_3_1","unstructured":"Ahmed M. (2014). Commercial crocodile farming in Bangladesh past present and future possibilities."},{"key":"e_1_3_3_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines10050691"},{"key":"e_1_3_3_5_1","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines10050665"},{"key":"e_1_3_3_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph19063729"},{"key":"e_1_3_3_7_1","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/139580"},{"key":"e_1_3_3_8_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph19137723"},{"key":"e_1_3_3_9_1","doi-asserted-by":"publisher","DOI":"10.1128\/ecosalplus.ESP-0009-2017"},{"key":"e_1_3_3_10_1","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2022.2153168"},{"key":"e_1_3_3_11_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0052773"},{"key":"e_1_3_3_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biologicals.2017.08.004"},{"key":"e_1_3_3_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-80899-6"},{"key":"e_1_3_3_14_1","volume-title":"Basic local alignment search tool","author":"Blast N.","year":"2015","unstructured":"Blast, N. (2015). Basic local alignment search tool. National Library of Medicine: National Center for Biotechnology Information."},{"key":"e_1_3_3_15_1","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.012419-0"},{"key":"e_1_3_3_16_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889802020502"},{"key":"e_1_3_3_17_1","first-page":"29","article-title":"The FF14SB force field","volume":"14","author":"Case D. A.","year":"2014","unstructured":"Case, D. A., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., Cheatham, T. E., III, Darden, T. A., Duke, R. E., & Gohlke, H. (2014). The FF14SB force field. Amber, 14, 29\u201331.","journal-title":"Amber"},{"key":"e_1_3_3_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep24373"},{"key":"e_1_3_3_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmii.2011.11.007"},{"key":"e_1_3_3_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki396"},{"key":"e_1_3_3_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki008"},{"key":"e_1_3_3_22_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00335-003-2296-6"},{"key":"e_1_3_3_23_1","doi-asserted-by":"publisher","DOI":"10.7774\/cevr.2014.3.1.50"},{"key":"e_1_3_3_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-90868-2"},{"key":"e_1_3_3_25_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00894-014-2278-5"},{"key":"e_1_3_3_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg231"},{"key":"e_1_3_3_27_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-4"},{"key":"e_1_3_3_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biologicals.2018.07.004"},{"key":"e_1_3_3_29_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-021-01301-0"},{"key":"e_1_3_3_30_1","doi-asserted-by":"publisher","DOI":"10.6026\/97320630008341"},{"key":"e_1_3_3_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04378-z"},{"key":"e_1_3_3_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp858"},{"key":"e_1_3_3_33_1","doi-asserted-by":"publisher","DOI":"10.1517\/17460441.2015.1032936"},{"key":"e_1_3_3_34_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00256"},{"key":"e_1_3_3_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki376"},{"key":"e_1_3_3_36_1","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines10020189"},{"key":"e_1_3_3_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq003"},{"key":"e_1_3_3_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_3_3_39_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejps.2020.105258"},{"key":"e_1_3_3_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2021.104705"},{"key":"e_1_3_3_41_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.1332996"},{"key":"e_1_3_3_42_1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00019-07"},{"key":"e_1_3_3_43_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.humimm.2020.05.010"},{"key":"e_1_3_3_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx346"},{"key":"e_1_3_3_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks493"},{"key":"e_1_3_3_46_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2016.169"},{"key":"e_1_3_3_47_1","doi-asserted-by":"publisher","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V"},{"key":"e_1_3_3_48_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci500020m"},{"key":"e_1_3_3_49_1","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.72.1.66-75.2004"},{"key":"e_1_3_3_50_1","doi-asserted-by":"publisher","DOI":"10.2174\/157016406780655568"},{"key":"e_1_3_3_51_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-005-0003-0"},{"key":"e_1_3_3_52_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9601-8_1"},{"key":"e_1_3_3_53_1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/161.3.525"},{"key":"e_1_3_3_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/s1359-6446(03)02689-8"},{"key":"e_1_3_3_55_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2015.03.027"},{"key":"e_1_3_3_56_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-2713-9"},{"issue":"2","key":"e_1_3_3_57_1","first-page":"86","article-title":"Biofilm bacteria: formation and comparative susceptibility to antibiotics","volume":"66","author":"Olson M. E.","year":"2002","unstructured":"Olson, M. E., Ceri, H., Morck, D. W., Buret, A. G., & Read, R. R. (2002). Biofilm bacteria: formation and comparative susceptibility to antibiotics. Canadian Journal of Veterinary Research\u2009=\u2009Revue Canadienne de Recherche Veterinaire, 66(2), 86\u201392.","journal-title":"Canadian Journal of Veterinary Research\u2009=\u2009Revue Canadienne de Recherche Veterinaire"},{"key":"e_1_3_3_58_1","unstructured":"ProtParam E. (2017). ExPASy-ProtParam tool."},{"key":"e_1_3_3_59_1","unstructured":"Rapin N. Lund O. & Castiglione F. (2012). C-Immsim 10.1 server."},{"key":"e_1_3_3_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/nm1129"},{"key":"e_1_3_3_61_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2017.05.001"},{"key":"e_1_3_3_62_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph19148408"},{"key":"e_1_3_3_63_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1540-0"},{"key":"e_1_3_3_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmgm.2019.107477"},{"key":"e_1_3_3_65_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00028"},{"key":"e_1_3_3_66_1","first-page":"383","volume-title":"Urinary tract infections: Molecular pathogenesis and clinical management","author":"Schaffer J. N.","year":"2017","unstructured":"Schaffer, J. N., & Pearson, M. M. (2017). Proteus mirabilis and urinary tract infections. In Urinary tract infections: Molecular pathogenesis and clinical management (pp. 383\u2013433)."},{"key":"e_1_3_3_67_1","unstructured":"Schafmeister C. Ross W. S. & Romanovski V. (1995). The leap module of AMBER. University of California."},{"key":"e_1_3_3_68_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2012.03939.x"},{"key":"e_1_3_3_69_1","first-page":"585","article-title":"Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease","volume":"1","author":"Shivanika C.","year":"2020","unstructured":"Shivanika, C., Kumar, D., Ragunathan, V., Tiwari, P., Sumitha., & A., Others. (2020). Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. Journal of Biomolecular Structure & Dynamics, 1, 585\u2013611.","journal-title":"Journal of Biomolecular Structure & Dynamics"},{"key":"e_1_3_3_70_1","doi-asserted-by":"publisher","DOI":"10.1080\/10408398.2017.1341864"},{"key":"e_1_3_3_71_1","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines3030579"},{"key":"e_1_3_3_72_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2021.104389"},{"key":"e_1_3_3_73_1","volume-title":"XMGRACE, Version 5.1. 19","author":"Turner P. J.","year":"2005","unstructured":"Turner, P. J. (2005). XMGRACE, Version 5.1. 19. Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology."},{"key":"e_1_3_3_74_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph182010961"},{"key":"e_1_3_3_75_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku938"},{"key":"e_1_3_3_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2017.12.063"},{"key":"e_1_3_3_77_1","first-page":"U403","article-title":"Antechamber: An accessory software package for molecular mechanical calculations","volume":"222","author":"Wang J.","year":"2001","unstructured":"Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2001). Antechamber: An accessory software package for molecular mechanical calculations. Journal of the American Chemical Society, 222, U403.","journal-title":"Journal of the American Chemical Society"},{"key":"e_1_3_3_78_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00414"},{"key":"e_1_3_3_79_1","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.1244"},{"key":"e_1_3_3_80_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq249"},{"key":"e_1_3_3_81_1","doi-asserted-by":"publisher","DOI":"10.4137\/DTI.S384_"}],"container-title":["Journal of Biomolecular Structure and Dynamics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.tandfonline.com\/doi\/pdf\/10.1080\/07391102.2022.2153920","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T16:30:36Z","timestamp":1719419436000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.tandfonline.com\/doi\/full\/10.1080\/07391102.2022.2153920"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,7]]},"references-count":80,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2023,11,24]]}},"alternative-id":["10.1080\/07391102.2022.2153920"],"URL":"https:\/\/doi.org\/10.1080\/07391102.2022.2153920","relation":{},"ISSN":["0739-1102","1538-0254"],"issn-type":[{"value":"0739-1102","type":"print"},{"value":"1538-0254","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,7]]},"assertion":[{"value":"The publishing and review policy for this title is described in its Aims & Scope.","order":1,"name":"peerreview_statement","label":"Peer Review Statement"},{"value":"http:\/\/www.tandfonline.com\/action\/journalInformation?show=aimsScope&journalCode=tbsd20","URL":"http:\/\/www.tandfonline.com\/action\/journalInformation?show=aimsScope&journalCode=tbsd20","order":2,"name":"aims_and_scope_url","label":"Aim & Scope"},{"value":"2022-07-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-25","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-12-07","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}