{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T12:51:23Z","timestamp":1740142283487,"version":"3.37.3"},"reference-count":86,"publisher":"American Chemical Society (ACS)","issue":"2","funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["LISBOA-01-0145-FEDER-007660"],"award-info":[{"award-number":["LISBOA-01-0145-FEDER-007660"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda??o para a Ci?ncia e a Tecnologia","doi-asserted-by":"publisher","award":["Pest-OE\/EQB\/LA0004\/2011","PTDC\/QEQ-COM\/1623\/2012","SFRH\/BD\/65709\/2009","SFRH\/BPD\/76621\/2011"],"award-info":[{"award-number":["Pest-OE\/EQB\/LA0004\/2011","PTDC\/QEQ-COM\/1623\/2012","SFRH\/BD\/65709\/2009","SFRH\/BPD\/76621\/2011"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2017,2,27]]},"DOI":"10.1021\/acs.jcim.6b00575","type":"journal-article","created":{"date-parts":[[2017,1,18]],"date-time":"2017-01-18T05:28:45Z","timestamp":1484717325000},"page":"256-266","source":"Crossref","is-referenced-by-count":5,"title":["Effect of a pH Gradient on the Protonation States of Cytochrome <i>c<\/i> Oxidase: A Continuum Electrostatics Study"],"prefix":"10.1021","volume":"57","author":[{"given":"Pedro R.","family":"Magalh\u00e3es","sequence":"first","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica\re Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal"}]},{"given":"A. Sofia F.","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica\re Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal"}]},{"given":"Sara R. R.","family":"Campos","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica\re Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal"}]},{"given":"Cl\u00e1udio M.","family":"Soares","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica\re Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7044-1210","authenticated-orcid":true,"given":"Ant\u00f3nio M.","family":"Baptista","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica\re Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal"}]}],"member":"316","published-online":{"date-parts":[[2017,1,31]]},"reference":[{"key":"ref1\/cit1","volume-title":"Bioenergetics","author":"Nicholls D. G.","year":"2002","edition":"3"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1016\/S0005-2728(01)00169-4"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1007\/s10863-008-9181-7"},{"key":"ref4\/cit4","unstructured":"DeLano, W.PyMOL Molecular Graphics System 2002."},{"key":"ref5\/cit5","unstructured":"GIMP 2.8.10,www.gimp.org, 1997\u20132016."},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.17.9085"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.2741\/4086"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1021\/bi026093+"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1021\/bi026750y"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2010.02.020"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1016\/S0005-2728(98)00075-9"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2635097100"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0611627104"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/bi971458p"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1023\/A:1020524014920"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2013.0183"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2013.03.001"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1111\/j.1432-1033.1969.tb19633.x"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1021\/bi00316a025"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1021\/bi501022j"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1021\/bi9606509"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2011.04.001"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.03.075"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1021\/ja0619657"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(99)77452-7"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/jp002763e"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0606149103"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2016.03.024"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(95)00042-E"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1021\/ct700301q"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360230807"},{"volume-title":"Numerical Recipes in C, the Art of Scientific Computing","year":"1992","author":"Press W.","key":"ref32\/cit32"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540141103"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540160303"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1007\/s00249-011-0700-9"},{"key":"ref36\/cit36","unstructured":"Berendsen, H.InMolecular Dynamics and Protein Structure: Proceedings of a Workshop Held 13\u201318 May 1984 at the University of North Carolina;Hermans, J., Ed.University of North Carolina, Distributed by Polycrystal Book Service:Western Springs, IL, 1985."},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1063\/1.469273"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1063\/1.2408420"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(92)91009-E"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1021\/jp052259f"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004010"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10643"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1002\/prot.1106"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1021\/ct5000082"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2008.03.016"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1063\/1.1699114"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.physiol.66.032102.150049"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.3027"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1993.1626"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1110\/ps.9.9.1753"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.29.1.291"},{"key":"ref54\/cit54","doi-asserted-by":"crossref","unstructured":"Eswar, N.; Webb, B.; Marti-Renom, M. A.; Madhusudhan, M. S.; Eramian, D.; Shen, M.Y.; Pieper, U.; Sali, A.Comparative Protein Structure Modeling Using Modeller.Curr. Protoc. Bioinform. 2006, Chapter 5, Unit 5.6.","DOI":"10.1002\/0471250953.bi0506s15"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(99)80118-X"},{"key":"ref56\/cit56","unstructured":"Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, N. J.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J.Gaussian 09, Revision A.1; 2009."},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1021\/j100142a004"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1002\/anie.200802019"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(98)73996-7"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(95)80406-6"},{"key":"ref61\/cit61","unstructured":"Williams, T.; Kelley, C.Gnuplot. 2004."},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1021\/bi9924821"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.20.10547"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1126\/science.280.5370.1723"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0800770105"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1021\/jp407250d"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1038\/376660a0"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(199801)30:1<100::AID-PROT9>3.3.CO;2-Q"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2014.08.003"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1021\/bi026524o"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2007.11.010"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2091-7-18"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1021\/ct8000014"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1021\/bi701614w"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M803511200"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1021\/ja993774s"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00619-8"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1007\/s00775-003-0509-9"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1021\/bi052183d"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.081088398"},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2006.05.041"},{"key":"ref82\/cit82","doi-asserted-by":"publisher","DOI":"10.1021\/j100233a010"},{"key":"ref83\/cit83","doi-asserted-by":"publisher","DOI":"10.1016\/0304-4173(85)90014-X"},{"key":"ref84\/cit84","doi-asserted-by":"publisher","DOI":"10.1007\/s007750100287"},{"key":"ref85\/cit85","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21588"},{"key":"ref86\/cit86","doi-asserted-by":"publisher","DOI":"10.1021\/ja209176e"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6b00575","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,25]],"date-time":"2023-04-25T16:49:56Z","timestamp":1682441396000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.6b00575"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,31]]},"references-count":86,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2017,2,27]]}},"alternative-id":["10.1021\/acs.jcim.6b00575"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6b00575","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"type":"print","value":"1549-9596"},{"type":"electronic","value":"1549-960X"}],"subject":[],"published":{"date-parts":[[2017,1,31]]}}}