{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,27]],"date-time":"2024-08-27T04:30:31Z","timestamp":1724733031622},"reference-count":55,"publisher":"Wiley","issue":"28","license":[{"start":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T00:00:00Z","timestamp":1561420800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM093937"],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2019,10,30]]},"abstract":"Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object\u2010oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large\u2010scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. \u00a9 2019 The Authors. Journal of Computational Chemistry<\/jats:italic> published by Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.26006","type":"journal-article","created":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T20:19:45Z","timestamp":1561493985000},"page":"2502-2508","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["DelPhi Suite: New Developments and Review of Functionalities"],"prefix":"10.1002","volume":"40","author":[{"given":"Chuan","family":"Li","sequence":"first","affiliation":[{"name":"Department of Mathematics West Chester University of Pennsylvania West Chester Pennsylvania 19383"}]},{"given":"Zhe","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Arghya","family":"Chakravorty","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Swagata","family":"Pahari","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Yunhui","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Sankar","family":"Basu","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Mahesh","family":"Koirala","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Shailesh Kumar","family":"Panday","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]},{"given":"Marharyta","family":"Petukh","sequence":"additional","affiliation":[{"name":"Department of Biology Presbyterian College Clinton South Carolina 29325"}]},{"given":"Lin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Physics University of Texas at EI Paso Texas 79968"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-5346-0156","authenticated-orcid":false,"given":"Emil","family":"Alexov","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy Clemson University Clemson South Carolina 29634"}]}],"member":"311","published-online":{"date-parts":[[2019,6,25]]},"reference":[{"key":"e_1_2_6_1_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr300461d"},{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.7761829"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1088\/1478-3975\/8\/3\/035001"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M113.457382"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmc.2009.07.071"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja042641q"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1432-1033.2003.03917.x"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00249-006-0123-1"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22931"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0033583513000024"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22786"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt032"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24218"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2012.05.013"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.23189"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(02)73940-4"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/bs.mie.2016.05.052"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.106.092122"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.107.125609"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1002\/bip.20877"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(04)83005-2"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00382"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.2478\/mlbmb-2013-0002"},{"key":"e_1_2_6_24_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct600085e"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.10378"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/2046-1682-5-9"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.1161"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cplett.2012.10.081"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2005.07.022"},{"key":"e_1_2_6_30_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3280"},{"key":"e_1_2_6_31_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20565"},{"key":"e_1_2_6_32_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20000"},{"key":"e_1_2_6_33_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17040512"},{"key":"e_1_2_6_34_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17040547"},{"key":"e_1_2_6_35_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004276"},{"key":"e_1_2_6_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx698"},{"key":"e_1_2_6_37_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.24935"},{"key":"e_1_2_6_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv607"},{"key":"e_1_2_6_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24715"},{"key":"e_1_2_6_40_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx495"},{"key":"e_1_2_6_41_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01429-15"},{"key":"e_1_2_6_42_1","doi-asserted-by":"publisher","DOI":"10.1142\/S0219633614400021"},{"key":"e_1_2_6_43_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct400065j"},{"key":"e_1_2_6_44_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2018.00025"},{"key":"e_1_2_6_45_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24831"},{"key":"e_1_2_6_46_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.langmuir.6b04430"},{"key":"e_1_2_6_47_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.25608"},{"key":"e_1_2_6_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2013.08.013"},{"key":"e_1_2_6_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2015.01.003"},{"key":"e_1_2_6_50_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.24968"},{"key":"e_1_2_6_51_1","doi-asserted-by":"publisher","DOI":"10.1002\/humu.22770"},{"key":"e_1_2_6_52_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2013.07.014"},{"key":"e_1_2_6_53_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj103"},{"key":"e_1_2_6_54_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep23249"},{"key":"e_1_2_6_55_1","doi-asserted-by":"publisher","DOI":"10.4208\/cicp.300611.201011s"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.26006","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26006","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jcc.26006","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26006","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,9]],"date-time":"2023-09-09T16:43:16Z","timestamp":1694277796000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.26006"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6,25]]},"references-count":55,"journal-issue":{"issue":"28","published-print":{"date-parts":[[2019,10,30]]}},"alternative-id":["10.1002\/jcc.26006"],"URL":"https:\/\/doi.org\/10.1002\/jcc.26006","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6,25]]},"assertion":[{"value":"2019-04-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-06-09","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-06-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}