{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T07:38:39Z","timestamp":1740123519009,"version":"3.37.3"},"reference-count":86,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2020,1,20]],"date-time":"2020-01-20T00:00:00Z","timestamp":1579478400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,20]],"date-time":"2020-01-20T00:00:00Z","timestamp":1579478400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21803057"],"award-info":[{"award-number":["21803057"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LR19B030001"],"award-info":[{"award-number":["LR19B030001"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2020,4]]},"DOI":"10.1007\/s10822-020-00282-5","type":"journal-article","created":{"date-parts":[[2020,1,20]],"date-time":"2020-01-20T06:02:42Z","timestamp":1579500162000},"page":"421-435","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields"],"prefix":"10.1007","volume":"34","author":[{"given":"Ye","family":"Ding","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"You","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Qian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinfeng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Houhou","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9639-2907","authenticated-orcid":false,"given":"Jing","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,1,20]]},"reference":[{"issue":"3","key":"282_CR1","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/nrd3078","volume":"9","author":"SM Paul","year":"2010","unstructured":"Paul SM, Mytelka DS, Dunwiddie CT, Persinger CC, Munos BH, Lindborg SR, Schacht AL (2010) How to improve r&d productivity: the pharmaceutical industry\u2019s grand challenge. Nat Rev Drug Discov 9(3):203","journal-title":"Nat Rev Drug Discov"},{"issue":"11","key":"282_CR2","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1007\/s10822-016-9954-8","volume":"30","author":"CC Bannan","year":"2016","unstructured":"Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL (2016) Blind prediction of cyclohexane-water distribution coefficients from the sampl5 challenge. J Comput Aided Mol Des 30(11):927\u2013944","journal-title":"J Comput Aided Mol Des"},{"issue":"11","key":"282_CR3","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1007\/s10822-016-9971-7","volume":"30","author":"AS Rustenburg","year":"2016","unstructured":"Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD (2016) Measuring experimental cyclohexane-water distribution coefficients for the sampl5 challenge. J Comput Aided Mol Des 30(11):945\u2013958","journal-title":"J Comput Aided Mol Des"},{"issue":"11","key":"282_CR4","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1007\/s10822-016-9955-7","volume":"30","author":"FC Pickard","year":"2016","unstructured":"Pickard FC, K\u00f6nig G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR (2016) Blind prediction of distribution in the sampl5 challenge with qm based protomer and pKa corrections. J Comput Aided Mol Des 30(11):1087\u20131100","journal-title":"J Comput Aided Mol Des"},{"issue":"11","key":"282_CR5","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1007\/s10822-016-9936-x","volume":"30","author":"G K\u00f6nig","year":"2016","unstructured":"K\u00f6nig G, Pickard FC, Huang J, Simmonett AC, Tofoleanu F, Lee J, Dral PO, Prasad S, Jones M, Shao Y et al (2016) Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of mm and qm\/mm explicit solvent simulations of water-cyclohexane transfer in the sampl5 challenge. J Comput Aided Mol Des 30(11):989\u20131006","journal-title":"J Comput Aided Mol Des"},{"key":"282_CR6","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-019-00271-3","author":"M I\u015f\u0131k","year":"2020","unstructured":"I\u015f\u0131k M, Levorse D, Mobley DL, Rhodes T, Chodera JD (2020) Octanol-water partition coefficient measurements for the sampl6 blind prediction challenge. J Comput Aided Mol Des.\u00a0https:\/\/doi.org\/10.1007\/s10822-019-00271-3","journal-title":"J Comput Aided Mol Des"},{"issue":"31","key":"282_CR7","doi-asserted-by":"publisher","first-page":"6810","DOI":"10.1021\/acs.jpcb.9b04061","volume":"123","author":"V Kundi","year":"2019","unstructured":"Kundi V, Ho J (2019) Predicting octanol-water partition coefficients: are quantum mechanical implicit solvent models better than empirical fragment-based methods? J Phys Chem B 123(31):6810\u20136822","journal-title":"J Phys Chem B"},{"key":"282_CR8","doi-asserted-by":"publisher","first-page":"3144","DOI":"10.1021\/jz501315h","volume":"5","author":"J Huang","year":"2014","unstructured":"Huang J, Lopes P, Roux B, MacKerell A (2014) Recent advances in polarizable force fields for macromolecules: microsecond simulations of proteins using the classical drude oscillator model. J Phys Chem Lett 5:3144\u20133150","journal-title":"J Phys Chem Lett"},{"key":"282_CR9","doi-asserted-by":"publisher","first-page":"4983","DOI":"10.1021\/acs.chemrev.5b00505","volume":"116","author":"J Lemkul","year":"2016","unstructured":"Lemkul J, Huang J, Roux B, MacKerell A (2016) An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications. Chem Rev 116:4983\u20135013","journal-title":"Chem Rev"},{"key":"282_CR10","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.sbi.2017.10.008","volume":"48","author":"J Huang","year":"2018","unstructured":"Huang J, MacKerell AD (2018) Force field development and simulations of intrinsically disordered proteins. Curr Opin Struct Biol 48:40\u201348","journal-title":"Curr Opin Struct Biol"},{"issue":"6","key":"282_CR11","doi-asserted-by":"publisher","first-page":"3854","DOI":"10.1021\/acs.jctc.9b00016","volume":"15","author":"A Kr\u00e4mer","year":"2019","unstructured":"Kr\u00e4mer A, Pickard FC, Huang J, Venable RM, Simmonett AC, Reith D, Kirschner KN, Pastor RW, Brooks BR (2019) Interactions of water and alkanes: modifying additive force fields to account for polarization effects. J Chem Theor Comput 15(6):3854\u20133867","journal-title":"J Chem Theor Comput"},{"issue":"3","key":"282_CR12","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1007\/s10822-014-9733-3","volume":"28","author":"F Manzoni","year":"2014","unstructured":"Manzoni F, S\u00f6derhjelm P (2014) Prediction of hydration free energies for the sampl4 data set with the amoeba polarizable force field. J Comput Aided Mol Des 28(3):235\u2013244","journal-title":"J Comput Aided Mol Des"},{"issue":"8","key":"282_CR13","doi-asserted-by":"publisher","first-page":"3871","DOI":"10.1021\/acs.jctc.6b00276","volume":"12","author":"RT Bradshaw","year":"2016","unstructured":"Bradshaw RT, Essex JW (2016) Evaluating parametrization protocols for hydration free energy calculations with the amoeba polarizable force field. J Chem Theor Comput 12(8):3871\u20133883","journal-title":"J Chem Theor Comput"},{"issue":"44","key":"282_CR14","doi-asserted-by":"publisher","first-page":"30261","DOI":"10.1039\/C6CP02509A","volume":"18","author":"DR Bell","year":"2016","unstructured":"Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P (2016) Calculating binding free energies of host-guest systems using the amoeba polarizable force field. Phys Chem Chem Phys 18(44):30261\u201330269","journal-title":"Phys Chem Chem Phys"},{"issue":"10","key":"282_CR15","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1007\/s10822-018-0147-5","volume":"32","author":"ML Laury","year":"2018","unstructured":"Laury ML, Wang Z, Gordon AS, Ponder JW (2018) Absolute binding free energies for the sampl6 cucurbit [8] uril host-guest challenge via the amoeba polarizable force field. J Comput Aided Mol Des 32(10):1087\u20131095","journal-title":"J Comput Aided Mol Des"},{"issue":"11","key":"282_CR16","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1007\/s10822-016-9958-4","volume":"30","author":"G Kamath","year":"2016","unstructured":"Kamath G, Kurnikov I, Fain B, Leontyev I, Illarionov A, Butin O, Olevanov M, Pereyaslavets L (2016) Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and arrow polarizable force fields. J Comput Aided Mol Des 30(11):977\u2013988","journal-title":"J Comput Aided Mol Des"},{"key":"282_CR17","doi-asserted-by":"publisher","first-page":"3025","DOI":"10.1063\/1.1589749","volume":"119","author":"G Lamoureux","year":"2003","unstructured":"Lamoureux G, Roux B (2003) Modeling induced polarization with classical drude oscillators: theory and molecular dynamics simulation algorithm. J Chem Phys 119:3025\u20133039","journal-title":"J Chem Phys"},{"key":"282_CR18","doi-asserted-by":"publisher","first-page":"5185","DOI":"10.1063\/1.1598191","volume":"119","author":"G Lamoureux","year":"2003","unstructured":"Lamoureux G, MacKerell AD, Roux B (2003) A simple polarizable model of water based on classical Drude oscillators. J Chem Phys 119:5185\u20135197","journal-title":"J Chem Phys"},{"key":"282_CR19","doi-asserted-by":"publisher","first-page":"5430","DOI":"10.1021\/ct400781b","volume":"9","author":"P Lopes","year":"2013","unstructured":"Lopes P, Huang J, Shim J, Luo Y, Li H, Roux B, MacKerell A (2013) Polarizable force field for peptides and proteins based on the classical drude oscillator. J Chem Theor Comput 9:5430\u20135449","journal-title":"J Chem Theor Comput"},{"issue":"5","key":"282_CR20","doi-asserted-by":"publisher","first-page":"2053","DOI":"10.1021\/acs.jctc.7b00067","volume":"13","author":"JA Lemkul","year":"2017","unstructured":"Lemkul JA, MacKerell AD Jr (2017) Polarizable force field for dna based on the classical drude oscillator: I. Refinement using quantum mechanical base stacking and conformational energetics. J Chem Theor Comput 13(5):2053\u20132071","journal-title":"J Chem Theor Comput"},{"issue":"5","key":"282_CR21","doi-asserted-by":"publisher","first-page":"2072","DOI":"10.1021\/acs.jctc.7b00068","volume":"13","author":"JA Lemkul","year":"2017","unstructured":"Lemkul JA, MacKerell AD Jr (2017) Polarizable force field for dna based on the classical drude oscillator: II. Microsecond molecular dynamics simulations of duplex DNA. J Chem Theor Comput 13(5):2072\u20132085","journal-title":"J Chem Theor Comput"},{"issue":"32","key":"282_CR22","doi-asserted-by":"publisher","first-page":"2624","DOI":"10.1002\/jcc.25709","volume":"39","author":"JA Lemkul","year":"2018","unstructured":"Lemkul JA, MacKerell AD Jr (2018) Polarizable force field for RNA based on the classical Drude oscillator. J Comput Chem 39(32):2624\u20132646","journal-title":"J Comput Chem"},{"issue":"31","key":"282_CR23","doi-asserted-by":"publisher","first-page":"9142","DOI":"10.1021\/jp402860e","volume":"117","author":"J Chowdhary","year":"2013","unstructured":"Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD Jr, Roux B (2013) A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B 117(31):9142\u20139160","journal-title":"J Phys Chem B"},{"issue":"9","key":"282_CR24","doi-asserted-by":"publisher","first-page":"4535","DOI":"10.1021\/acs.jctc.7b00262","volume":"13","author":"H Li","year":"2017","unstructured":"Li H, Chowdhary J, Huang L, He X, MacKerell AD Jr, Roux B (2017) Drude polarizable force field for molecular dynamics simulations of saturated and unsaturated Zwitterionic lipids. J Chem Theor Comput 13(9):4535\u20134552","journal-title":"J Chem Theor Comput"},{"issue":"3","key":"282_CR25","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1021\/jp412696m","volume":"119","author":"DS Patel","year":"2014","unstructured":"Patel DS, He X, MacKerell AD Jr (2014) Polarizable empirical force field for hexopyranose monosaccharides based on the classical drude oscillator. J Phys Chem B 119(3):637\u2013652","journal-title":"J Phys Chem B"},{"issue":"4","key":"282_CR26","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1007\/s10822-017-0010-0","volume":"31","author":"MC Small","year":"2017","unstructured":"Small MC, Aytenfisu AH, Lin FY, He X, MacKerell AD (2017) Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des 31(4):349\u2013363","journal-title":"J Comput Aided Mol Des"},{"issue":"3","key":"282_CR27","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1021\/ct900576a","volume":"6","author":"H Yu","year":"2010","unstructured":"Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, MacKerell AD Jr, Roux B (2010) Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field. J Chem Theor Comput 6(3):774\u2013786","journal-title":"J Chem Theor Comput"},{"issue":"44","key":"282_CR28","doi-asserted-by":"publisher","first-page":"11436","DOI":"10.1021\/acs.jpcb.6b09262","volume":"120","author":"JA Lemkul","year":"2016","unstructured":"Lemkul JA, MacKerell AD Jr (2016) Balancing the interactions of mg2+ in aqueous solution and with nucleic acid moieties for a polarizable force field based on the classical Drude oscillator model. J Phys Chem B 120(44):11436\u201311448","journal-title":"J Phys Chem B"},{"issue":"5","key":"282_CR29","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1021\/acs.jcim.8b00132","volume":"58","author":"FY Lin","year":"2018","unstructured":"Lin FY, Lopes PE, Harder E, Roux B, MacKerell AD Jr (2018) Polarizable force field for molecular ions based on the classical Drude oscillator. J Chem Inf Model 58(5):993\u20131004","journal-title":"J Chem Inf Model"},{"issue":"2","key":"282_CR30","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1021\/jz101461d","volume":"2","author":"W Jiang","year":"2010","unstructured":"Jiang W, Hardy DJ, Phillips JC, MacKerell AD Jr, Schulten K, Roux B (2010) High-performance scalable molecular dynamics simulations of a polarizable force field based on classical drude oscillators in NAMD. J Phys Chem Lett 2(2):87\u201392","journal-title":"J Phys Chem Lett"},{"issue":"1","key":"282_CR31","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1021\/acs.jcim.5b00612","volume":"56","author":"A Dequidt","year":"2015","unstructured":"Dequidt A, Devemy J, Padua AA (2015) Thermalized drude oscillators with the LAMMPS molecular dynamics simulator. J Chem Inf Model 56(1):260\u2013268","journal-title":"J Chem Inf Model"},{"issue":"19","key":"282_CR32","doi-asserted-by":"publisher","first-page":"1473","DOI":"10.1002\/jcc.23937","volume":"36","author":"JA Lemkul","year":"2015","unstructured":"Lemkul JA, Roux B, van der Spoel D, MacKerell AD Jr (2015) Implementation of extended Lagrangian dynamics in gromacs for polarizable simulations using the classical Drude oscillator model. J Comp Chem 36(19):1473\u20131479","journal-title":"J Comp Chem"},{"issue":"21","key":"282_CR33","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1002\/jcc.25339","volume":"39","author":"J Huang","year":"2018","unstructured":"Huang J, Lemkul JA, Eastman PK, MacKerell AD Jr (2018) Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: implementation, validation, and benchmarks. J Comput Chem 39(21):1682\u20131689","journal-title":"J Comput Chem"},{"issue":"10","key":"282_CR34","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1007\/s10822-018-0166-2","volume":"32","author":"N Nishikawa","year":"2018","unstructured":"Nishikawa N, Han K, Wu X, Tofoleanu F, Brooks BR (2018) Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for sampl6 octa-acid host-guest challenges. J Comput Aided Mol Des 32(10):1075\u20131086","journal-title":"J Comput Aided Mol Des"},{"issue":"11","key":"282_CR35","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1007\/s10822-016-9964-6","volume":"30","author":"MR Jones","year":"2016","unstructured":"Jones MR, Brooks BR, Wilson AK (2016) Partition coefficients for the SAMPL5 challenge using transfer free energies. J Comput Aided Mol Des 30(11):1129\u20131138","journal-title":"J Comput Aided Mol Des"},{"key":"282_CR36","volume-title":"Gaussian$$^{}\\sim $$16 Revision C.01","author":"MJ Frisch","year":"2016","unstructured":"Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN, Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, Fox DJ (2016) Gaussian$$^{}\\sim$$16 Revision C.01. Gaussian Inc., Wallingford"},{"issue":"2","key":"282_CR37","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1063\/1.456153","volume":"90","author":"TH Dunning Jr","year":"1989","unstructured":"Dunning TH Jr (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys 90(2):1007\u20131023","journal-title":"J Chem Phys"},{"issue":"2","key":"282_CR38","doi-asserted-by":"publisher","first-page":"1358","DOI":"10.1063\/1.464303","volume":"98","author":"DE Woon","year":"1993","unstructured":"Woon DE, Dunning TH Jr (1993) Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. J Chem Phys 98(2):1358\u20131371","journal-title":"J Chem Phys"},{"issue":"11","key":"282_CR39","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1063\/1.470645","volume":"103","author":"DE Woon","year":"1995","unstructured":"Woon DE, Dunning TH Jr (1995) Gaussian basis sets for use in correlated molecular calculations. V. Core-valence basis sets for boron through neon. J Chem Phys 103(11):4572\u20134585","journal-title":"J Chem Phys"},{"issue":"4","key":"282_CR40","doi-asserted-by":"publisher","first-page":"2975","DOI":"10.1063\/1.466439","volume":"100","author":"DE Woon","year":"1994","unstructured":"Woon DE, Dunning TH Jr (1994) Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties. J Chem Phys 100(4):2975\u20132988","journal-title":"J Chem Phys"},{"key":"282_CR41","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/jcc.540040211","volume":"4","author":"BR Brooks","year":"1983","unstructured":"Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187\u2013217","journal-title":"J Comp Chem"},{"issue":"10","key":"282_CR42","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks","year":"2009","unstructured":"Brooks BR, Brooks CL III, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S et al (2009) CHARMM: the biomolecular simulation program. J Comp Chem 30(10):1545\u20131614","journal-title":"J Comp Chem"},{"key":"282_CR43","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.commatsci.2019.05.003","volume":"167","author":"M Girard","year":"2019","unstructured":"Girard M, Ehlen A, Shakya A, Bereau T, de la Cruz MO (2019) Hoobas: a highly object-oriented builder for molecular dynamics. Comput Mater Sci 167:25\u201333","journal-title":"Comput Mater Sci"},{"issue":"1","key":"282_CR44","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.cplett.2005.10.135","volume":"418","author":"G Lamoureux","year":"2006","unstructured":"Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD (2006) A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 418(1):245\u2013249","journal-title":"Chem Phys Lett"},{"issue":"6","key":"282_CR45","doi-asserted-by":"publisher","first-page":"1927","DOI":"10.1021\/ct700100a","volume":"3","author":"VM Anisimov","year":"2007","unstructured":"Anisimov VM, Vorobyov IV, Roux B, MacKerell AD (2007) Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theor Comput 3(6):1927\u20131946","journal-title":"J Chem Theor Comput"},{"issue":"40","key":"282_CR46","doi-asserted-by":"publisher","first-page":"18988","DOI":"10.1021\/jp053182y","volume":"109","author":"IV Vorobyov","year":"2005","unstructured":"Vorobyov IV, Anisimov VM, MacKerell AD (2005) Polarizable empirical force field for alkanes based on the classical Drude oscillator model. J Phys Chem B 109(40):18988\u201318999","journal-title":"J Phys Chem B"},{"issue":"12","key":"282_CR47","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an Nlog (N) method for Ewald sums in large systems. J Chem Phys 98(12):10089\u201310092","journal-title":"J Chem Phys"},{"issue":"5","key":"282_CR48","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1080\/00268977700102571","volume":"34","author":"W Van Gunsteren","year":"1977","unstructured":"Van Gunsteren W, Berendsen H (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 34(5):1311\u20131327","journal-title":"Mol Phys"},{"issue":"1","key":"282_CR49","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1021\/acs.jctc.5b00935","volume":"12","author":"J Lee","year":"2015","unstructured":"Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y et al (2015) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM\/OpenMM simulations using the CHARMM36 additive force field. J Chem Theor Comput 12(1):405\u2013413","journal-title":"J Chem Theor Comput"},{"issue":"7","key":"282_CR50","doi-asserted-by":"publisher","first-page":"e1005659","DOI":"10.1371\/journal.pcbi.1005659","volume":"13","author":"P Eastman","year":"2017","unstructured":"Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD et al (2017) OpenMM 7: rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol 13(7):e1005659","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"282_CR51","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1080\/00268979600100761","volume":"87","author":"GJ Martyna","year":"1996","unstructured":"Martyna GJ, Tuckerman ME, Tobias DJ, Klein ML (1996) Explicit reversible integrators for extended systems dynamics. Mol Phys 87(5):1117\u20131157","journal-title":"Mol Phys"},{"issue":"1","key":"282_CR52","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1063\/1.447334","volume":"81","author":"S Nos\u00e9","year":"1984","unstructured":"Nos\u00e9 S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81(1):511\u2013519","journal-title":"J Chem Phys"},{"issue":"15","key":"282_CR53","doi-asserted-by":"publisher","first-page":"6042","DOI":"10.1063\/1.1308516","volume":"113","author":"Y Sugita","year":"2000","unstructured":"Sugita Y, Kitao A, Okamoto Y (2000) Multidimensional replica-exchange method for free-energy calculations. J Chem Phys 113(15):6042\u20136051","journal-title":"J Chem Phys"},{"issue":"12","key":"282_CR54","doi-asserted-by":"publisher","first-page":"9025","DOI":"10.1063\/1.466707","volume":"100","author":"M Zacharias","year":"1994","unstructured":"Zacharias M, Straatsma T, McCammon J (1994) Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J Chem Phys 100(12):9025\u20139031","journal-title":"J Chem Phys"},{"issue":"10","key":"282_CR55","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.3390\/molecules23102695","volume":"23","author":"G K\u00f6nig","year":"2018","unstructured":"K\u00f6nig G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM (2018) A comparison of qm\/mm simulations with and without the drude oscillator model based on hydration free energies of simple solutes. Molecules 23(10):2695","journal-title":"Molecules"},{"issue":"12","key":"282_CR56","doi-asserted-by":"publisher","first-page":"124105","DOI":"10.1063\/1.2978177","volume":"129","author":"MR Shirts","year":"2008","unstructured":"Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129(12):124105","journal-title":"J Chem Phys"},{"issue":"5","key":"282_CR57","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1007\/s10822-015-9840-9","volume":"29","author":"PV Klimovich","year":"2015","unstructured":"Klimovich PV, Shirts MR, Mobley DL (2015) Guidelines for the analysis of free energy calculations. J Comput Aided Mol Des 29(5):397\u2013411","journal-title":"J Comput Aided Mol Des"},{"issue":"45","key":"282_CR58","doi-asserted-by":"publisher","first-page":"13052","DOI":"10.1021\/jp0735987","volume":"111","author":"MR Shirts","year":"2007","unstructured":"Shirts MR, Mobley DL, Chodera JD, Pande VS (2007) Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B 111(45):13052\u201313063","journal-title":"J Phys Chem B"},{"issue":"12","key":"282_CR59","doi-asserted-by":"publisher","first-page":"5737","DOI":"10.1021\/acs.jctc.5b00726","volume":"11","author":"CL Wennberg","year":"2015","unstructured":"Wennberg CL, Murtola T, P\u00e1ll S, Abraham MJ, Hess B, Lindahl E (2015) Direct-space corrections enable fast and accurate Lorentz-Berthelot combination rule Lennard-Jones lattice summation. J Chem Theor Comput 11(12):5737\u20135746","journal-title":"J Chem Theor Comput"},{"issue":"2","key":"282_CR60","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1021\/acs.jctc.7b00948","volume":"14","author":"AN Leonard","year":"2018","unstructured":"Leonard AN, Simmonett AC, Pickard FC, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW (2018) Comparison of additive and polarizable models with explicit treatment of long-range Lennard-Jones interactions using alkane simulations. J Chem Theor Comput 14(2):948\u2013958","journal-title":"J Chem Theor Comput"},{"issue":"8","key":"282_CR61","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1063\/1.1740409","volume":"22","author":"RW Zwanzig","year":"1954","unstructured":"Zwanzig RW (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 22(8):1420\u20131426","journal-title":"J Chem Phys"},{"issue":"6","key":"282_CR62","doi-asserted-by":"publisher","first-page":"3098","DOI":"10.1103\/PhysRevA.38.3098","volume":"38","author":"AD Becke","year":"1988","unstructured":"Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38(6):3098","journal-title":"Phys Rev A"},{"issue":"2","key":"282_CR63","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1103\/PhysRevB.37.785","volume":"37","author":"C Lee","year":"1988","unstructured":"Lee C, Yang W, Parr RG (1988) Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37(2):785","journal-title":"Phys Rev B"},{"issue":"18","key":"282_CR64","doi-asserted-by":"publisher","first-page":"6378","DOI":"10.1021\/jp810292n","volume":"113","author":"AV Marenich","year":"2009","unstructured":"Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113(18):6378\u20136396","journal-title":"J Phys Chem B"},{"issue":"7","key":"282_CR65","doi-asserted-by":"publisher","first-page":"5648","DOI":"10.1063\/1.464913","volume":"98","author":"AD Becke","year":"1993","unstructured":"Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98(7):5648\u20135652","journal-title":"J Chem Phys"},{"issue":"21","key":"282_CR66","doi-asserted-by":"publisher","first-page":"9244","DOI":"10.1063\/1.1367373","volume":"114","author":"TH Dunning Jr","year":"2001","unstructured":"Dunning TH Jr, Peterson KA, Wilson AK (2001) Gaussian basis sets for use in correlated molecular calculations. X. The atoms aluminum through argon revisited. J Chem Phys 114(21):9244\u20139253","journal-title":"J Chem Phys"},{"issue":"2","key":"282_CR67","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1080\/00268976.2014.952696","volume":"113","author":"Y Shao","year":"2015","unstructured":"Shao Y, Gan Z, Epifanovsky E, Gilbert AT, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X et al (2015) Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol Phys 113(2):184\u2013215","journal-title":"Mol Phys"},{"issue":"9","key":"282_CR68","doi-asserted-by":"publisher","first-page":"1485","DOI":"10.1002\/jcc.20587","volume":"28","author":"HL Woodcock III","year":"2007","unstructured":"Woodcock HL III, Hodo\u0161\u010dek M, Gilbert AT, Gill PM, Schaefer HF III, Brooks BR (2007) Interfacing q-chem and charmm to perform qm\/mm reaction path calculations. J Comp Chem 28(9):1485\u20131502","journal-title":"J Comp Chem"},{"issue":"22","key":"282_CR69","doi-asserted-by":"publisher","first-page":"224107","DOI":"10.1063\/1.3665893","volume":"135","author":"SJ Fox","year":"2011","unstructured":"Fox SJ, Pittock C, Fox T, Tautermann CS, Skylaris CK (2011) Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules. J Chem Phys 135(22):224107","journal-title":"J Chem Phys"},{"issue":"4","key":"282_CR70","doi-asserted-by":"publisher","first-page":"2193","DOI":"10.1063\/1.455064","volume":"89","author":"GA Petersson","year":"1988","unstructured":"Petersson GA, Bennett A, Tensfeldt TG, Al-Laham MA, Shirley WA, Mantzaris J (1988) A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements. J Chem Phys 89(4):2193\u20132218","journal-title":"J Chem Phys"},{"issue":"3","key":"282_CR71","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1007\/s10822-014-9717-3","volume":"28","author":"S Genheden","year":"2014","unstructured":"Genheden S, Martinez AIC, Criddle MP, Essex JW (2014) Extensive all-atom monte carlo sampling and qm\/mm corrections in the sampl4 hydration free energy challenge. J Comput Aided Mol Des 28(3):187\u2013200","journal-title":"J Comput Aided Mol Des"},{"key":"282_CR72","first-page":"E-52","volume-title":"CRC handbook of chemistry and physics","author":"RC Weast","year":"1988","unstructured":"Weast RC, Astle MJ, Beyer WH et\u00a0al (1988) CRC handbook of chemistry and physics, vol\u00a069. CRC Press, Boca Raton, p E-52"},{"issue":"36","key":"282_CR73","doi-asserted-by":"publisher","first-page":"18017","DOI":"10.1021\/jp062614h","volume":"110","author":"F Palombo","year":"2006","unstructured":"Palombo F, Sassi P, Paolantoni M, Morresi A, Cataliotti RS (2006) Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques. J Phys Chem B 110(36):18017\u201318025","journal-title":"J Phys Chem B"},{"issue":"8","key":"282_CR74","doi-asserted-by":"publisher","first-page":"2221","DOI":"10.1021\/je3001427","volume":"57","author":"BE Lang","year":"2012","unstructured":"Lang BE (2012) Solubility of water in octan-1-ol from (275 to 369) k. J Chem Eng Data 57(8):2221\u20132226","journal-title":"J Chem Eng Data"},{"issue":"9","key":"282_CR75","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"J Wang","year":"2004","unstructured":"Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comp Chem 25(9):1157\u20131174","journal-title":"J Comp Chem"},{"issue":"4","key":"282_CR76","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"K Vanommeslaeghe","year":"2010","unstructured":"Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I et al (2010) Charmm general force field: a force field for drug-like molecules compatible with the charmm all-atom additive biological force fields. J Comp Chem 31(4):671\u2013690","journal-title":"J Comp Chem"},{"issue":"8","key":"282_CR77","doi-asserted-by":"publisher","first-page":"3543","DOI":"10.1021\/ct4003477","volume":"9","author":"L Huang","year":"2013","unstructured":"Huang L, Roux B (2013) Automated force field parameterization for nonpolarizable and polarizable atomic models based on ab initio target data. J Chem Theor Comput 9(8):3543\u20133556","journal-title":"J Chem Theor Comput"},{"issue":"2","key":"282_CR78","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1021\/acs.jctc.6b01125","volume":"13","author":"J Huang","year":"2017","unstructured":"Huang J, Mei Y, K\u00f6nig G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y (2017) An estimation of hybrid quantum mechanical molecular mechanical polarization energies for small molecules using polarizable force-field approaches. J Chem Theor Comput 13(2):679\u2013695","journal-title":"J Chem Theor Comput"},{"issue":"161","key":"282_CR79","first-page":"702","volume":"147","author":"J Huang","year":"2017","unstructured":"Huang J, Simmonett AC, Pickard FC, MacKerell AD, Brooks BR (2017) Mapping the drude polarizable force field onto a multipole and induced dipole model. J Chem Phys 147(161):702","journal-title":"J Chem Phys"},{"issue":"22","key":"282_CR80","doi-asserted-by":"publisher","first-page":"224,107","DOI":"10.1063\/1.4953558","volume":"144","author":"H Wang","year":"2016","unstructured":"Wang H, Yang W (2016) Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory. J Chem Phys 144(22):224,107","journal-title":"J Chem Phys"},{"issue":"4","key":"282_CR81","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1021\/ct401118k","volume":"10","author":"G K\u00f6nig","year":"2014","unstructured":"K\u00f6nig G, Hudson PS, Boresch S, Woodcock HL (2014) Multiscale free energy simulations: an efficient method for connecting classical md simulations to qm or qm\/mm free energies using non-boltzmann bennett reweighting schemes. J Chem Theor Comput 10(4):1406\u20131419","journal-title":"J Chem Theor Comput"},{"issue":"11","key":"282_CR82","doi-asserted-by":"publisher","first-page":"5583","DOI":"10.1021\/acs.jctc.8b00571","volume":"14","author":"P Li","year":"2018","unstructured":"Li P, Jia X, Pan X, Shao Y, Mei Y (2018) Accelerated computation of free energy profile at ab initio quantum mechanical\/molecular mechanics accuracy via a semi-empirical reference potential. I. Weighted thermodynamics perturbation. J Chem Theor Comput 14(11):5583\u20135596","journal-title":"J Chem Theor Comput"},{"key":"282_CR83","doi-asserted-by":"publisher","first-page":"20595","DOI":"10.1039\/C9CP02593F","volume":"21","author":"X Pan","year":"2019","unstructured":"Pan X, Li P, Ho J, Pu J, Mei Y, Shao Y (2019) Accelerated computation of free energy profile at ab initio quantum mechanical\/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching. Phys Chem Chem Phys 21:20595\u201320605","journal-title":"Phys Chem Chem Phys"},{"issue":"6","key":"282_CR84","doi-asserted-by":"publisher","first-page":"2954","DOI":"10.1021\/acs.jctc.7b00016","volume":"13","author":"A Ganguly","year":"2017","unstructured":"Ganguly A, Boulanger E, Thiel W (2017) Importance of mm polarization in qm\/mm studies of enzymatic reactions: assessment of the qm\/mm drude oscillator model. J Chem Theor Comput 13(6):2954\u20132961","journal-title":"J Chem Theor Comput"},{"issue":"11","key":"282_CR85","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1002\/jcc.24295","volume":"37","author":"EG Kratz","year":"2016","unstructured":"Kratz EG, Walker AR, Lagard\u00e8re L, Lipparini F, Piquemal JP, Andr\u00e9s Cisneros G (2016) Lichem: a qm\/mm program for simulations with multipolar and polarizable force fields. J Comp Chem 37(11):1019\u20131029","journal-title":"J Comp Chem"},{"issue":"12","key":"282_CR86","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1063\/1.4962909","volume":"145","author":"J Dziedzic","year":"2016","unstructured":"Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK (2016) Tinktep: a fully self-consistent, mutually polarizable qm\/mm approach based on the amoeba force field. J Chem Phys 145(12):124106","journal-title":"J Chem Phys"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-020-00282-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-020-00282-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-020-00282-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T10:05:27Z","timestamp":1722333927000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-020-00282-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,20]]},"references-count":86,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,4]]}},"alternative-id":["282"],"URL":"https:\/\/doi.org\/10.1007\/s10822-020-00282-5","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2020,1,20]]},"assertion":[{"value":"12 October 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 January 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 January 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}