{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:26:53Z","timestamp":1772119613912,"version":"3.50.1"},"reference-count":136,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T00:00:00Z","timestamp":1580083200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T00:00:00Z","timestamp":1580083200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30 CA008748"],"award-info":[{"award-number":["P30 CA008748"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01GM108889-01"],"award-info":[{"award-number":["1R01GM108889-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01GM124270-01A1"],"award-info":[{"award-number":["1R01GM124270-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM061300"],"award-info":[{"award-number":["GM061300"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM130794"],"award-info":[{"award-number":["R01GM130794"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CHE 1352608"],"award-info":[{"award-number":["CHE 1352608"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS 1761320"],"award-info":[{"award-number":["DMS 1761320"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BioExcel CoE","award":["H2020-INFRAEDI-02-2018-823830"],"award-info":[{"award-number":["H2020-INFRAEDI-02-2018-823830"]}]},{"name":"Greek Research & Technology Network","award":["vspr001005\/arp2\/3"],"award-info":[{"award-number":["vspr001005\/arp2\/3"]}]},{"name":"OPENSCREEN-GR","award":["MIS 5002691"],"award-info":[{"award-number":["MIS 5002691"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2020,5]]},"DOI":"10.1007\/s10822-020-00290-5","type":"journal-article","created":{"date-parts":[[2020,1,26]],"date-time":"2020-01-26T22:02:25Z","timestamp":1580076145000},"page":"601-633","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":99,"title":["The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations"],"prefix":"10.1007","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7693-2013","authenticated-orcid":false,"given":"Andrea","family":"Rizzi","sequence":"first","affiliation":[]},{"given":"Travis","family":"Jensen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3928-5050","authenticated-orcid":false,"given":"David R.","family":"Slochower","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0019-8806","authenticated-orcid":false,"given":"Matteo","family":"Aldeghi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6761-7780","authenticated-orcid":false,"given":"Vytautas","family":"Gapsys","sequence":"additional","affiliation":[]},{"given":"Dimitris","family":"Ntekoumes","sequence":"additional","affiliation":[]},{"given":"Stefano","family":"Bosisio","sequence":"additional","affiliation":[]},{"given":"Michail","family":"Papadourakis","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7916-0757","authenticated-orcid":false,"given":"Niel M.","family":"Henriksen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3570-3534","authenticated-orcid":false,"given":"Bert L.","family":"de Groot","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9287-364X","authenticated-orcid":false,"given":"Zoe","family":"Cournia","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9640-1380","authenticated-orcid":false,"given":"Alex","family":"Dickson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0360-1760","authenticated-orcid":false,"given":"Julien","family":"Michel","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3375-1738","authenticated-orcid":false,"given":"Michael K.","family":"Gilson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3249-1097","authenticated-orcid":false,"given":"Michael R.","family":"Shirts","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1083-5533","authenticated-orcid":false,"given":"David L.","family":"Mobley","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0542-119X","authenticated-orcid":false,"given":"John D.","family":"Chodera","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,1,27]]},"reference":[{"key":"290_CR1","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511730412.007","author":"MR Shirts","year":"2010","unstructured":"Shirts MR, Mobley DL, Brown SP (2010) Free-energy calculations in structure-based drug design. Drug Des. https:\/\/doi.org\/10.1017\/CBO9780511730412.007","journal-title":"Drug Des"},{"issue":"6","key":"290_CR2","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1021\/acs.jmedchem.6b01881","volume":"60","author":"B Kuhn","year":"2017","unstructured":"Kuhn B, Tich\u00fd M, Wang L, Robinson S, Martin RE, Kuglstatter A, Benz J (2017) Prospective evaluation of free energy calculations for the prioritization of cathepsin L inhibitors. J Med Chem 60(6):2485\u20132497","journal-title":"J Med Chem"},{"issue":"9","key":"290_CR3","doi-asserted-by":"crossref","first-page":"1856","DOI":"10.1021\/acs.jcim.6b00220","volume":"56","author":"M Ciordia","year":"2016","unstructured":"Ciordia M, P\u00e9rez-Benito L, Delgado F, Trabanco AA, Tresadern G (2016) Application of free energy perturbation for the design of BACE1 inhibitors. J Chem Inf Model 56(9):1856\u20131871","journal-title":"J Chem Inf Model"},{"issue":"1","key":"290_CR4","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1007\/s10822-017-0064-z","volume":"32","author":"C Schindler","year":"2018","unstructured":"Schindler C, Rippmann F, Kuhn D (2018) Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+. J Comput Aided Mol Des 32(1):265\u2013272","journal-title":"J Comput Aided Mol Des"},{"issue":"7","key":"290_CR5","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1021\/ja512751q","volume":"137","author":"L Wang","year":"2015","unstructured":"Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J et al (2015) Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc 137(7):2695\u20132703","journal-title":"J Am Chem Soc"},{"key":"290_CR6","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.26036","author":"DD Minh","year":"2019","unstructured":"Minh DD (2019) Alchemical Grid Dock (AlGDock): binding free energy calculations between flexible ligands and rigid receptors. J Comput Chem. https:\/\/doi.org\/10.1002\/jcc.26036","journal-title":"J Comput Chem"},{"key":"290_CR7","doi-asserted-by":"crossref","first-page":"3495","DOI":"10.1021\/acs.jpclett.9b01183","volume":"10","author":"R Capelli","year":"2019","unstructured":"Capelli R, Carloni P, Parrinello M (2019) Exhaustive search of ligand binding pathways via volume-based metadynamics. J Phys Chem Lett 10:3495\u20133499","journal-title":"J Phys Chem Lett"},{"issue":"6","key":"290_CR8","doi-asserted-by":"crossref","first-page":"3218","DOI":"10.1021\/acs.jctc.8b00027","volume":"14","author":"BW Irwin","year":"2018","unstructured":"Irwin BW, Huggins DJ (2018) Estimating atomic contributions to hydration and binding using free energy perturbation. J Chem Theory Comput 14(6):3218\u20133227","journal-title":"J Chem Theory Comput"},{"issue":"12","key":"290_CR9","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1007\/s10822-016-9996-y","volume":"30","author":"B Sherborne","year":"2016","unstructured":"Sherborne B, Shanmugasundaram V, Cheng AC, Christ CD, DesJarlais RL, Duca JS, Lewis RA, Loughney DA, Manas ES, McGaughey GB et al (2016) Collaborating to improve the use of free-energy and other quantitative methods in drug discovery. J Comput Aided Mol Des 30(12):1139\u20131141","journal-title":"J Comput Aided Mol Des"},{"issue":"12","key":"290_CR10","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1021\/acs.jcim.7b00564","volume":"57","author":"Z Cournia","year":"2017","unstructured":"Cournia Z, Allen B, Sherman W (2017) Relative binding free energy calculations in drug discovery: recent advances and practical considerations. J Chem Inf Model 57(12):2911\u20132937","journal-title":"J Chem Inf Model"},{"key":"290_CR11","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1146\/annurev-biophys-070816-033654","volume":"46","author":"DL Mobley","year":"2017","unstructured":"Mobley DL, Gilson MK (2017) Predicting binding free energies: frontiers and benchmarks. Annu Rev Biophys 46:531\u2013558","journal-title":"Annu Rev Biophys"},{"issue":"9","key":"290_CR12","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1007\/s10822-016-9946-8","volume":"30","author":"S Gathiaka","year":"2016","unstructured":"Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA et al (2016) D3R grand challenge 2015: evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des 30(9):651\u2013668","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"290_CR13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10822-017-0088-4","volume":"32","author":"Z Gaieb","year":"2018","unstructured":"Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG et al (2018) D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des 32(1):1\u201320","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"290_CR14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10822-018-0180-4","volume":"33","author":"Z Gaieb","year":"2019","unstructured":"Gaieb Z, Parks CD, Chiu M, Yang H, Shao C, Walters WP, Lambert MH, Nevins N, Bembenek SD, Ameriks MK et al (2019) D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J Comput Aided Mol Des 33(1):1\u201318","journal-title":"J Comput Aided Mol Des"},{"issue":"3","key":"290_CR15","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1016\/S0006-3495(97)78756-3","volume":"72","author":"MK Gilson","year":"1997","unstructured":"Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 72(3):1047\u20131069. https:\/\/doi.org\/10.1016\/S0006-3495(97)78756-3","journal-title":"Biophys J"},{"issue":"20","key":"290_CR16","doi-asserted-by":"crossref","first-page":"12562","DOI":"10.1073\/pnas.202427399","volume":"99","author":"A Laio","year":"2002","unstructured":"Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci 99(20):12562\u201312566","journal-title":"Proc Natl Acad Sci"},{"issue":"2","key":"290_CR17","doi-asserted-by":"crossref","first-page":"020603","DOI":"10.1103\/PhysRevLett.100.020603","volume":"100","author":"A Barducci","year":"2008","unstructured":"Barducci A, Bussi G, Parrinello M (2008) Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys Rev Lett 100(2):020603","journal-title":"Phys Rev Lett"},{"issue":"21","key":"290_CR18","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1103\/PhysRevLett.57.2607","volume":"57","author":"RH Swendsen","year":"1986","unstructured":"Swendsen RH, Wang JS (1986) Replica Monte Carlo simulation of spin-glasses. Phys Rev Lett 57(21):2607","journal-title":"Phys Rev Lett"},{"issue":"6","key":"290_CR19","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.1143\/JPSJ.65.1604","volume":"65","author":"K Hukushima","year":"1996","unstructured":"Hukushima K, Nemoto K (1996) Exchange Monte Carlo method and application to spin glass simulations. J Phys Soc Jpn 65(6):1604\u20131608","journal-title":"J Phys Soc Jpn"},{"issue":"15","key":"290_CR20","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. https:\/\/doi.org\/10.1063\/1.1308516","journal-title":"J Chem Phys"},{"issue":"3","key":"290_CR21","doi-asserted-by":"crossref","first-page":"1776","DOI":"10.1063\/1.462133","volume":"96","author":"A Lyubartsev","year":"1992","unstructured":"Lyubartsev A, Martsinovski A, Shevkunov S, Vorontsov-Velyaminov P (1992) New approach to Monte Carlo calculation of the free energy: method of expanded ensembles. J Chem Phys 96(3):1776\u20131783","journal-title":"J Chem Phys"},{"issue":"1","key":"290_CR22","first-page":"34","volume":"2013","author":"B Leimkuhler","year":"2012","unstructured":"Leimkuhler B, Matthews C (2012) Rational construction of stochastic numerical methods for molecular sampling. Appl Math Res Express 2013(1):34\u201356","journal-title":"Appl Math Res Express"},{"issue":"5","key":"290_CR23","doi-asserted-by":"crossref","first-page":"318","DOI":"10.3390\/e20050318","volume":"20","author":"J Fass","year":"2018","unstructured":"Fass J, Sivak D, Crooks G, Beauchamp K, Leimkuhler B, Chodera J (2018) Quantifying configuration-sampling error in Langevin simulations of complex molecular systems. Entropy 20(5):318","journal-title":"Entropy"},{"issue":"14","key":"290_CR24","doi-asserted-by":"crossref","first-page":"144107","DOI":"10.1063\/1.1873592","volume":"122","author":"MR Shirts","year":"2005","unstructured":"Shirts MR, Pande VS (2005) Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys 122(14):144107","journal-title":"J Chem Phys"},{"issue":"1","key":"290_CR25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10822-016-9974-4","volume":"31","author":"J Yin","year":"2017","unstructured":"Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK (2017) Overview of the SAMPL5 host\u2013guest challenge: are we doing better? J Comput Aided Mol Des 31(1):1\u201319","journal-title":"J Comput Aided Mol Des"},{"issue":"10","key":"290_CR26","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1007\/s10822-018-0170-6","volume":"32","author":"A Rizzi","year":"2018","unstructured":"Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL et al (2018) Overview of the SAMPL6 host\u2013guest binding affinity prediction challenge. J Comput Aided Mol Des 32(10):937\u2013963","journal-title":"J Comput Aided Mol Des"},{"issue":"6","key":"290_CR27","doi-asserted-by":"crossref","first-page":"3279","DOI":"10.1021\/acs.jctc.8b00031","volume":"14","author":"I Cabeza de Vaca","year":"2018","unstructured":"Cabeza de Vaca I, Qian Y, Vilseck JZ, Tirado-Rives J, Jorgensen WL (2018) Enhanced Monte Carlo methods for modeling proteins including computation of absolute free energies of binding. J Chem Theory Comput 14(6):3279\u20133288","journal-title":"J Chem Theory Comput"},{"issue":"25","key":"290_CR28","doi-asserted-by":"crossref","first-page":"17081","DOI":"10.1039\/C8CP01524D","volume":"20","author":"N Deng","year":"2018","unstructured":"Deng N, Cui D, Zhang BW, Xia J, Cruz J, Levy R (2018) Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. Phys Chem Chem Phys 20(25):17081\u201317092","journal-title":"Phys Chem Chem Phys"},{"key":"290_CR29","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-016-9977-1","author":"MR Shirts","year":"2016","unstructured":"Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED (2016) Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. https:\/\/doi.org\/10.1007\/s10822-016-9977-1","journal-title":"J Comput Aided Mol Des"},{"issue":"11","key":"290_CR30","doi-asserted-by":"crossref","first-page":"5567","DOI":"10.1021\/acs.jctc.8b00544","volume":"14","author":"HH Loeffler","year":"2018","unstructured":"Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J (2018) Reproducibility of free energy calculations across different molecular simulation software packages. J Chem Theory Comput 14(11):5567\u20135582","journal-title":"J Chem Theory Comput"},{"issue":"1","key":"290_CR31","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1039\/C5SC02678D","volume":"7","author":"M Aldeghi","year":"2016","unstructured":"Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC (2016) Accurate calculation of the absolute free energy of binding for drug molecules. Chem Sci 7(1):207\u2013218","journal-title":"Chem Sci"},{"issue":"1","key":"290_CR32","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1021\/acs.jctc.6b00979","volume":"13","author":"AP Bhati","year":"2016","unstructured":"Bhati AP, Wan S, Wright DW, Coveney PV (2016) Rapid, accurate, precise, and reliable relative free energy prediction using ensemble based thermodynamic integration. J Chem Theory Comput 13(1):210\u2013222","journal-title":"J Chem Theory Comput"},{"issue":"6","key":"290_CR33","doi-asserted-by":"crossref","first-page":"2930","DOI":"10.1021\/acs.jctc.6b01183","volume":"13","author":"B Xie","year":"2017","unstructured":"Xie B, Nguyen TH, Minh DD (2017) Absolute binding free energies between T4 lysozyme and 141 small molecules: calculations based on multiple rigid receptor configurations. J Chem Theory Comput 13(6):2930\u20132944","journal-title":"J Chem Theory Comput"},{"issue":"9","key":"290_CR34","doi-asserted-by":"crossref","first-page":"4253","DOI":"10.1021\/acs.jctc.7b00359","volume":"13","author":"NM Henriksen","year":"2017","unstructured":"Henriksen NM, Gilson MK (2017) Evaluating force field performance in thermodynamic calculations of cyclodextrin host\u2013guest binding: water models, partial charges, and host force field parameters. J Chem Theory Comput 13(9):4253\u20134269","journal-title":"J Chem Theory Comput"},{"issue":"21","key":"290_CR35","doi-asserted-by":"crossref","first-page":"5579","DOI":"10.1021\/acs.jpcb.7b11820","volume":"122","author":"SC Gill","year":"2018","unstructured":"Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL (2018) Binding modes of ligands using enhanced sampling (BLUES): rapid decorrelation of ligand binding modes via nonequilibrium candidate Monte Carlo. J Phys Chem B 122(21):5579\u20135598","journal-title":"J Phys Chem B"},{"issue":"8","key":"290_CR36","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1021\/acs.jctc.5b00436","volume":"11","author":"Y Miao","year":"2015","unstructured":"Miao Y, Feher VA, McCammon JA (2015) Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation. J Chem Theory Comput 11(8):3584\u20133595","journal-title":"J Chem Theory Comput"},{"issue":"12","key":"290_CR37","doi-asserted-by":"crossref","first-page":"124120","DOI":"10.1063\/1.3697833","volume":"136","author":"TT Pham","year":"2012","unstructured":"Pham TT, Shirts MR (2012) Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. J Chem Phys 136(12):124120","journal-title":"J Chem Phys"},{"issue":"19","key":"290_CR38","doi-asserted-by":"crossref","first-page":"194101","DOI":"10.1063\/1.4983164","volume":"146","author":"M Ath\u00e8nes","year":"2017","unstructured":"Ath\u00e8nes M, Terrier P (2017) Estimating thermodynamic expectations and free energies in expanded ensemble simulations: systematic variance reduction through conditioning. J Chem Phys 146(19):194101","journal-title":"J Chem Phys"},{"issue":"5","key":"290_CR39","doi-asserted-by":"crossref","first-page":"2154","DOI":"10.1021\/acs.jctc.6b00060","volume":"12","author":"TH Nguyen","year":"2016","unstructured":"Nguyen TH, Minh DD (2016) Intermediate thermodynamic states contribute equally to free energy convergence: a demonstration with replica exchange. J Chem Theory Comput 12(5):2154\u20132161","journal-title":"J Chem Theory Comput"},{"issue":"4","key":"290_CR40","doi-asserted-by":"crossref","first-page":"046705","DOI":"10.1103\/PhysRevE.80.046705","volume":"80","author":"DK Shenfeld","year":"2009","unstructured":"Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE (2009) Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations. Phys Rev E 80(4):046705","journal-title":"Phys Rev E"},{"issue":"21","key":"290_CR41","doi-asserted-by":"crossref","first-page":"5448","DOI":"10.1021\/acs.jpcb.7b11778","volume":"122","author":"JL MacCallum","year":"2018","unstructured":"MacCallum JL, Muniyat MI, Gaalswyk K (2018) Online optimization of total acceptance in Hamiltonian replica exchange simulations. J Phys Chem B 122(21):5448\u20135457","journal-title":"J Phys Chem B"},{"issue":"2","key":"290_CR42","doi-asserted-by":"crossref","first-page":"023312","DOI":"10.1103\/PhysRevE.98.023312","volume":"98","author":"V Lindahl","year":"2018","unstructured":"Lindahl V, Lidmar J, Hess B (2018) Riemann metric approach to optimal sampling of multidimensional free-energy landscapes. Phys Rev E 98(2):023312","journal-title":"Phys Rev E"},{"issue":"1","key":"290_CR43","doi-asserted-by":"crossref","first-page":"013207","DOI":"10.1088\/1742-5468\/aaf323","volume":"2019","author":"A Martinsson","year":"2019","unstructured":"Martinsson A, Lu J, Leimkuhler B, Vanden-Eijnden E (2019) The simulated tempering method in the infinite switch limit with adaptive weight learning. J Stat Mech Theory Exp 2019(1):013207","journal-title":"J Stat Mech Theory Exp"},{"issue":"10","key":"290_CR44","doi-asserted-by":"crossref","first-page":"100602","DOI":"10.1103\/PhysRevLett.99.100602","volume":"99","author":"GE Crooks","year":"2007","unstructured":"Crooks GE (2007) Measuring thermodynamic length. Phys Rev Lett 99(10):100602","journal-title":"Phys Rev Lett"},{"issue":"19","key":"290_CR45","doi-asserted-by":"crossref","first-page":"190602","DOI":"10.1103\/PhysRevLett.108.190602","volume":"108","author":"DA Sivak","year":"2012","unstructured":"Sivak DA, Crooks GE (2012) Thermodynamic metrics and optimal paths. Phys Rev Lett 108(19):190602","journal-title":"Phys Rev Lett"},{"issue":"3","key":"290_CR46","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/s10822-014-9722-6","volume":"28","author":"RG Coleman","year":"2014","unstructured":"Coleman RG, Sterling T, Weiss DR (2014) SAMPL4 & DOCK3. 7: lessons for automated docking procedures. J Comput Aided Mol Des 28(3):201\u2013209","journal-title":"J Comput Aided Mol Des"},{"issue":"10","key":"290_CR47","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1007\/s10822-018-0159-1","volume":"32","author":"Y Eken","year":"2018","unstructured":"Eken Y, Patel P, D\u00edaz T, Jones MR, Wilson AK (2018) SAMPL6 host\u2013guest challenge: binding free energies via a multistep approach. J Comput Aided Mol Des 32(10):1097\u20131115","journal-title":"J Comput Aided Mol Des"},{"issue":"10","key":"290_CR48","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1007\/s10822-018-0165-3","volume":"32","author":"PS Hudson","year":"2018","unstructured":"Hudson PS, Han K, Woodcock HL, Brooks BR (2018) Force matching as a stepping stone to QM\/MM CB [8] host\/guest binding free energies: a SAMPL6 cautionary tale. J Comput Aided Mol Des 32(10):983\u2013999","journal-title":"J Comput Aided Mol Des"},{"issue":"5","key":"290_CR49","first-page":"2245","volume":"13","author":"MA Olsson","year":"2017","unstructured":"Olsson MA, Ryde U (2017) Comparison of QM\/MM methods to obtain ligand-binding free energies. J Comput Aided Mol Des 13(5):2245\u20132253","journal-title":"J Comput Aided Mol Des"},{"issue":"12","key":"290_CR50","first-page":"5526","volume":"9","author":"Z Zheng","year":"2013","unstructured":"Zheng Z, Ucisik MN, Merz KM (2013) The movable type method applied to protein-ligand binding. J Comput Aided Mol Des 9(12):5526\u20135538","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"290_CR51","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s10822-016-9980-6","volume":"31","author":"N Bansal","year":"2017","unstructured":"Bansal N, Zheng Z, Cerutti DS, Merz KM (2017) On the fly estimation of host\u2013guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. J Comput Aided Mol Des 31(1):47\u201360","journal-title":"J Comput Aided Mol Des"},{"key":"290_CR52","volume-title":"Guidelines for the treatment of malaria","author":"World Health Organization","year":"2015","unstructured":"World Health Organization (2015) Guidelines for the treatment of malaria. World Health Organization, Geneva"},{"issue":"37","key":"290_CR53","doi-asserted-by":"crossref","first-page":"11408","DOI":"10.1021\/ja0475611","volume":"126","author":"CL Gibb","year":"2004","unstructured":"Gibb CL, Gibb BC (2004) Well-defined, organic nanoenvironments in water: the hydrophobic effect drives a capsular assembly. J Am Chem Soc 126(37):11408\u201311409","journal-title":"J Am Chem Soc"},{"issue":"16","key":"290_CR54","doi-asserted-by":"crossref","first-page":"4048","DOI":"10.1021\/acs.orglett.6b01903","volume":"18","author":"MB Hillyer","year":"2016","unstructured":"Hillyer MB, Gibb CL, Sokkalingam P, Jordan JH, Ioup SE, Gibb BC (2016) Synthesis of water-soluble deep-cavity cavitands. Org Lett 18(16):4048\u20134051","journal-title":"Org Lett"},{"issue":"45","key":"290_CR55","doi-asserted-by":"crossref","first-page":"15959","DOI":"10.1021\/ja055013x","volume":"127","author":"S Liu","year":"2005","unstructured":"Liu S, Ruspic C, Mukhopadhyay P, Chakrabarti S, Zavalij PY, Isaacs L (2005) The cucurbit [n] uril family: prime components for self-sorting systems. J Am Chem Soc 127(45):15959\u201315967","journal-title":"J Am Chem Soc"},{"key":"290_CR56","doi-asserted-by":"crossref","unstructured":"Mobley DL, Heinzelmann G, Henriksen NM, Gilson MK (2017) Predicting binding free energies: frontiers and benchmarks (a perpetual review). Department of Pharmaceutical Sciences, UCI, Irvine. https:\/\/escholarship.org\/uc\/item\/9p37m6bq","DOI":"10.1101\/074625"},{"issue":"5","key":"290_CR57","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1007\/s10822-012-9544-3","volume":"26","author":"HS Muddana","year":"2012","unstructured":"Muddana HS, Gilson MK (2012) Prediction of SAMPL3 host\u2013guest binding affinities: evaluating the accuracy of generalized force-fields. J Comput Aided Mol Des 26(5):517\u2013525","journal-title":"J Comput Aided Mol Des"},{"issue":"4","key":"290_CR58","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/s10822-014-9735-1","volume":"28","author":"HS Muddana","year":"2014","unstructured":"Muddana HS, Fenley AT, Mobley DL, Gilson MK (2014) The SAMPL4 host\u2013guest blind prediction challenge: an overview. J Comput Aided Mol Des 28(4):305\u2013317","journal-title":"J Comput Aided Mol Des"},{"issue":"33","key":"290_CR59","doi-asserted-by":"crossref","first-page":"10272","DOI":"10.1021\/jp804429n","volume":"112","author":"J Ewell","year":"2008","unstructured":"Ewell J, Gibb BC, Rick SW (2008) Water inside a hydrophobic cavitand molecule. J Phys Chem B 112(33):10272\u201310279","journal-title":"J Phys Chem B"},{"issue":"1","key":"290_CR60","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1021\/ct300515n","volume":"9","author":"KE Rogers","year":"2012","unstructured":"Rogers KE, Ortiz-S\u00e1nchez JM, Baron R, Fajer M, de Oliveira CAF, McCammon JA (2012) On the role of dewetting transitions in host\u2013guest binding free energy calculations. J Chem Theory Comput 9(1):46\u201353. https:\/\/doi.org\/10.1021\/ct300515n","journal-title":"J Chem Theory Comput"},{"issue":"8","key":"290_CR61","doi-asserted-by":"crossref","first-page":"084902","DOI":"10.1063\/1.2221683","volume":"125","author":"DL Mobley","year":"2006","unstructured":"Mobley DL, Chodera JD, Dill KA (2006) On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys 125(8):084902","journal-title":"J Chem Phys"},{"issue":"12","key":"290_CR62","doi-asserted-by":"crossref","first-page":"6346","DOI":"10.1021\/acs.jctc.8b00825","volume":"14","author":"W Chen","year":"2018","unstructured":"Chen W, Deng Y, Russell E, Wu Y, Abel R, Wang L (2018) Accurate calculation of relative binding free energies between ligands with different net charges. J Chem Theory Comput 14(12):6346\u20136358","journal-title":"J Chem Theory Comput"},{"issue":"18","key":"290_CR63","doi-asserted-by":"crossref","first-page":"11B606-1","DOI":"10.1063\/1.4826261","volume":"139","author":"GJ Rocklin","year":"2013","unstructured":"Rocklin GJ, Mobley DL, Dill KA, H\u00fcnenberger PH (2013) Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys 139(18):11B606-1","journal-title":"J Chem Phys"},{"issue":"7","key":"290_CR64","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1021\/ct500195p","volume":"10","author":"YL Lin","year":"2014","unstructured":"Lin YL, Aleksandrov A, Simonson T, Roux B (2014) An overview of electrostatic free energy computations for solutions and proteins. J Chem Theory Comput 10(7):2690\u20132709","journal-title":"J Chem Theory Comput"},{"issue":"6","key":"290_CR65","doi-asserted-by":"crossref","first-page":"1884","DOI":"10.1021\/ct900565e","volume":"6","author":"BR Morgan","year":"2010","unstructured":"Morgan BR, Massi F (2010) Accurate estimates of free energy changes in charge mutations. J Chem Theory Comput 6(6):1884\u20131893","journal-title":"J Chem Theory Comput"},{"issue":"3","key":"290_CR66","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1021\/ci100436p","volume":"51","author":"M McGann","year":"2011","unstructured":"McGann M (2011) FRED pose prediction and virtual screening accuracy. J Chem Inf Model 51(3):578\u2013596. https:\/\/doi.org\/10.1021\/ci100436p","journal-title":"J Chem Inf Model"},{"issue":"8","key":"290_CR67","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1007\/s10822-012-9584-8","volume":"26","author":"M McGann","year":"2012","unstructured":"McGann M (2012) FRED and HYBRID docking performance on standardized datasets. J Comput Aided Mol Des 26(8):897\u2013906. https:\/\/doi.org\/10.1007\/s10822-012-9584-8","journal-title":"J Comput Aided Mol Des"},{"issue":"2","key":"290_CR68","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P","volume":"21","author":"A Jakalian","year":"2000","unstructured":"Jakalian A, Bush BL, Jack DB, Bayly CI (2000) Fast, efficient generation of high-quality atomic. Charges AM1-BCC model: I. Method. J Comput Chem 21(2):132\u2013146","journal-title":"J Comput Chem"},{"issue":"16","key":"290_CR69","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1002\/jcc.10128","volume":"23","author":"A Jakalian","year":"2002","unstructured":"Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23(16):1623\u20131641. https:\/\/doi.org\/10.1002\/jcc.10128","journal-title":"J Comput Chem"},{"issue":"9","key":"290_CR70","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 Comput Chem 25(9):1157\u20131174. https:\/\/doi.org\/10.1002\/jcc.20035","journal-title":"J Comput Chem"},{"issue":"2","key":"290_CR71","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926\u2013935. https:\/\/doi.org\/10.1063\/1.445869","journal-title":"J Chem Phys"},{"key":"290_CR72","volume-title":"AMBER 18","author":"D Case","year":"2018","unstructured":"Case D, Ben-Shalom I, Brozell S, Cerutti D, Cheatham T III, Cruzeiro V, Darden T, Duke R, Ghoreishi D, Gilson M, Gohlke H, Goetz A, Greene D, Harris R, Homeyer N, Izadi S, Kovalenko A, Kurtzman T, Lee T et al (2018) AMBER 18. University of California, San Francisco"},{"key":"290_CR73","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R, P\u00e1ll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19\u201325","journal-title":"SoftwareX"},{"issue":"16","key":"290_CR74","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"JC Phillips","year":"2005","unstructured":"Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781\u20131802","journal-title":"J Comput Chem"},{"issue":"7","key":"290_CR75","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 Computat Biol 13(7):e1005659. https:\/\/doi.org\/10.1371\/journal.pcbi.1005659","journal-title":"PLoS Computat Biol"},{"issue":"10","key":"290_CR76","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1007\/s10822-018-0154-6","volume":"32","author":"M Papadourakis","year":"2018","unstructured":"Papadourakis M, Bosisio S, Michel J (2018) Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge. J Comput Aided Mol Des 32(10):1047\u20131058","journal-title":"J Comput Aided Mol Des"},{"issue":"10","key":"290_CR77","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1007\/s10822-018-0149-3","volume":"32","author":"T Dixon","year":"2018","unstructured":"Dixon T, Lotz SD, Dickson A (2018) Predicting ligand binding affinity using on-and off-rates for the SAMPL6 SAMPLing challenge. J Comput Aided Mol Des 32(10):1001\u20131012","journal-title":"J Comput Aided Mol Des"},{"issue":"12","key":"290_CR78","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. https:\/\/doi.org\/10.1063\/1.2978177","journal-title":"J Chem Phys"},{"key":"290_CR79","doi-asserted-by":"publisher","unstructured":"Rizzi A, Chodera J, Naden L, Beauchamp K, Grinaway P, Rustenburg B, Albanese S, Saladi S (2018) choderalab\/yank: 0.20.1: exact treatment of PME electrostatics and optimizations. https:\/\/doi.org\/10.5281\/zenodo.1161274","DOI":"10.5281\/zenodo.1161274"},{"issue":"12","key":"290_CR80","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1007\/s10822-013-9689-8","volume":"27","author":"K Wang","year":"2013","unstructured":"Wang K, Chodera JD, Yang Y, Shirts MR (2013) Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des 27(12):989\u20131007","journal-title":"J Comput Aided Mol Des"},{"issue":"6","key":"290_CR81","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/0009-2614(94)00397-1","volume":"222","author":"TC Beutler","year":"1994","unstructured":"Beutler TC, Mark AE, van Schaik RC, Gerber PR, Van Gunsteren WF (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem Phys Lett 222(6):529\u2013539","journal-title":"Chem Phys Lett"},{"issue":"19","key":"290_CR82","doi-asserted-by":"crossref","first-page":"194110","DOI":"10.1063\/1.3660669","volume":"135","author":"JD Chodera","year":"2011","unstructured":"Chodera JD, Shirts MR (2011) Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. J Chem Phys 135(19):194110","journal-title":"J Chem Phys"},{"issue":"18","key":"290_CR83","doi-asserted-by":"crossref","first-page":"184107","DOI":"10.1063\/1.4712023","volume":"136","author":"C Desgranges","year":"2012","unstructured":"Desgranges C, Delhommelle J (2012) Evaluation of the grand-canonical partition function using expanded Wang\u2013Landau simulations. I. Thermodynamic properties in the bulk and at the liquid-vapor phase boundary. J Chem Phys 136(18):184107","journal-title":"J Chem Phys"},{"issue":"10","key":"290_CR84","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1103\/PhysRevLett.86.2050","volume":"86","author":"F Wang","year":"2001","unstructured":"Wang F, Landau D (2001) Efficient, multiple-range random walk algorithm to calculate the density of states. Phys Rev Lett 86(10):2050","journal-title":"Phys Rev Lett"},{"key":"290_CR85","unstructured":"Woods CJ, Mey AS, Calabro G, Julien M (2019) Sire molecular simulation framework. https:\/\/siremol.org"},{"issue":"4","key":"290_CR86","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1063\/1.439486","volume":"72","author":"HC Andersen","year":"1980","unstructured":"Andersen HC (1980) Molecular dynamics simulations at constant pressure and\/or temperature. J Chem Phys 72(4):2384\u20132393","journal-title":"J Chem Phys"},{"issue":"13","key":"290_CR87","doi-asserted-by":"crossref","first-page":"5451","DOI":"10.1063\/1.469273","volume":"102","author":"IG Tironi","year":"1995","unstructured":"Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102(13):5451\u20135459","journal-title":"J Chem Phys"},{"issue":"3","key":"290_CR88","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1080\/00268977300102101","volume":"26","author":"J Barker","year":"1973","unstructured":"Barker J, Watts R (1973) Monte Carlo studies of the dielectric properties of water-like models. Mol Phys 26(3):789\u2013792","journal-title":"Mol Phys"},{"key":"290_CR89","unstructured":"Bernardi R, Bhandarkar M, Bhatele BAA, Brunner R, Buelens F, Chipot C, Dalke A, Dixit S, Fiorin G, Freddolino P, Fu H, Grayson P, Gullingsrud J, Gursoy A, Hardy D, Harrison C, H\u00e9nin J, Humphrey W, Hurwitz D, Hynninen A, et al (2019) NAMD User\u2019s guide. Version 2.12"},{"key":"290_CR90","doi-asserted-by":"crossref","unstructured":"Gapsys V, Michielssens S, Peters JH, de Groot BL, Leonov H (2015) Calculation of binding free energies. In: Molecular modeling of proteins. Springer, New York, pp 173\u2013209","DOI":"10.1007\/978-1-4939-1465-4_9"},{"issue":"35","key":"290_CR91","doi-asserted-by":"publisher","first-page":"9535","DOI":"10.1021\/jp0217839","volume":"107","author":"S Boresch","year":"2003","unstructured":"Boresch S, Tettinger F, Leitgeb M, Karplus M (2003) Absolute binding free energies: a quantitative approach for their calculation. J Phys Chem B 107(35):9535\u20139551. https:\/\/doi.org\/10.1021\/jp0217839","journal-title":"J Phys Chem B"},{"issue":"3","key":"290_CR92","doi-asserted-by":"crossref","first-page":"2721","DOI":"10.1103\/PhysRevE.60.2721","volume":"60","author":"GE Crooks","year":"1999","unstructured":"Crooks GE (1999) Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys Rev E 60(3):2721","journal-title":"Phys Rev E"},{"issue":"27","key":"290_CR93","doi-asserted-by":"crossref","first-page":"2360","DOI":"10.1002\/jcc.23398","volume":"34","author":"C Velez-Vega","year":"2013","unstructured":"Velez-Vega C, Gilson MK (2013) Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J Comput Chem 34(27):2360\u20132371","journal-title":"J Comput Chem"},{"issue":"9","key":"290_CR94","doi-asserted-by":"crossref","first-page":"4377","DOI":"10.1021\/acs.jctc.5b00405","volume":"11","author":"NM Henriksen","year":"2015","unstructured":"Henriksen NM, Fenley AT, Gilson MK (2015) Computational calorimetry: high-precision calculation of host\u2013guest binding thermodynamics. J Chem Theory Comput 11(9):4377\u20134394","journal-title":"J Chem Theory Comput"},{"key":"290_CR95","doi-asserted-by":"crossref","first-page":"244112","DOI":"10.1063\/1.5100521","volume":"150","author":"N Donyapour","year":"2019","unstructured":"Donyapour N, Roussey NM, Dickson A (2019) REVO: resampling of ensembles by variation optimization. J Chem Phys 150:244112","journal-title":"J Chem Phys"},{"issue":"19","key":"290_CR96","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103(19):8577\u20138593. https:\/\/doi.org\/10.1063\/1.470117","journal-title":"J Chem Phys"},{"issue":"4","key":"290_CR97","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1021\/acs.jctc.8b01142","volume":"15","author":"W You","year":"2019","unstructured":"You W, Tang Z, Chang CeA (2019) Potential mean force from umbrella sampling simulations: what can we learn and what is missed? J Chem Theory Comput 15(4):2433\u20132443","journal-title":"J Chem Theory Comput"},{"issue":"10","key":"290_CR98","doi-asserted-by":"crossref","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\u2013guest challenge via the AMOEBA polarizable force field. J Comput Aided Mol Des 32(10):1087\u20131095","journal-title":"J Comput Aided Mol Des"},{"issue":"397","key":"290_CR99","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1080\/01621459.1987.10478410","volume":"82","author":"B Efron","year":"1987","unstructured":"Efron B (1987) Better bootstrap confidence intervals. J Am Stat Assoc 82(397):171\u2013185","journal-title":"J Am Stat Assoc"},{"issue":"4","key":"290_CR100","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1007\/s10822-014-9716-4","volume":"28","author":"JI Monroe","year":"2014","unstructured":"Monroe JI, Shirts MR (2014) Converging free energies of binding in cucurbit [7] uril and octa-acid host\u2013guest systems from SAMPL4 using expanded ensemble simulations. J Comput Aided Mol Des 28(4):401\u2013415","journal-title":"J Comput Aided Mol Des"},{"issue":"3","key":"290_CR101","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1103\/PhysRevE.61.2361","volume":"61","author":"GE Crooks","year":"2000","unstructured":"Crooks GE (2000) Path-ensemble averages in systems driven far from equilibrium. Phys Rev E 61(3):2361","journal-title":"Phys Rev E"},{"issue":"17","key":"290_CR102","doi-asserted-by":"crossref","first-page":"7330","DOI":"10.1063\/1.1363668","volume":"114","author":"G Hummer","year":"2001","unstructured":"Hummer G (2001) Fast-growth thermodynamic integration: error and efficiency analysis. J Chem Phys 114(17):7330\u20137337","journal-title":"J Chem Phys"},{"issue":"14","key":"290_CR103","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1103\/PhysRevLett.78.2690","volume":"78","author":"C Jarzynski","year":"1997","unstructured":"Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78(14):2690","journal-title":"Phys Rev Lett"},{"issue":"1\u20133","key":"290_CR104","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/0010-4655(95)00059-O","volume":"91","author":"KH Chow","year":"1995","unstructured":"Chow KH, Ferguson DM (1995) Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling. Comput Phys Commun 91(1\u20133):283\u2013289","journal-title":"Comput Phys Commun"},{"issue":"4\u20136","key":"290_CR105","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.cplett.2003.12.039","volume":"384","author":"J \u00c5qvist","year":"2004","unstructured":"\u00c5qvist J, Wennerstr\u00f6m P, Nervall M, Bjelic S, Brandsdal BO (2004) Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm. Chem Phys Lett 384(4\u20136):288\u2013294","journal-title":"Chem Phys Lett"},{"issue":"8","key":"290_CR106","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","volume":"81","author":"HJ Berendsen","year":"1984","unstructured":"Berendsen HJ, van Gunsteren WF, DiNola A, Haak J (1984) Postma Jv, molecular dynamics with coupling to an external bath. J Chem Phys 81(8):3684\u20133690","journal-title":"J Chem Phys"},{"issue":"9","key":"290_CR107","doi-asserted-by":"crossref","first-page":"e0202764","DOI":"10.1371\/journal.pone.0202764","volume":"13","author":"PT Merz","year":"2018","unstructured":"Merz PT, Shirts MR (2018) Testing for physical validity in molecular simulations. PLoS ONE 13(9):e0202764","journal-title":"PLoS ONE"},{"issue":"2","key":"290_CR108","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1021\/ct300688p","volume":"9","author":"MR Shirts","year":"2013","unstructured":"Shirts MR (2013) Simple quantitative tests to validate sampling from thermodynamic ensembles. J Chem Theory Comput 9(2):909\u2013926","journal-title":"J Chem Theory Comput"},{"key":"290_CR109","volume-title":"Theory of point estimation","author":"EL Lehmann","year":"2006","unstructured":"Lehmann EL, Casella G (2006) Theory of point estimation. Springer, New York"},{"issue":"1","key":"290_CR110","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1146\/annurev-biophys-083012-130318","volume":"42","author":"JD Chodera","year":"2013","unstructured":"Chodera JD, Mobley DL (2013) Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu Rev Biophys 42(1):121\u2013142. https:\/\/doi.org\/10.1146\/annurev-biophys-083012-130318","journal-title":"Annu Rev Biophys"},{"issue":"1","key":"290_CR111","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1021\/ct0502864","volume":"3","author":"JD Chodera","year":"2007","unstructured":"Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA (2007) Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J Chem Theory Comput 3(1):26\u201341","journal-title":"J Chem Theory Comput"},{"issue":"3","key":"290_CR112","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1080\/10610278.2018.1516885","volume":"31","author":"S Murkli","year":"2019","unstructured":"Murkli S, McNeill JN, Isaacs L (2019) Cucurbit [8] uril \u00b7 guest complexes: blinded dataset for the SAMPL6 challenge. Supramol Chem 31(3):150\u2013158","journal-title":"Supramol Chem"},{"issue":"3","key":"290_CR113","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1080\/10610278.2018.1549327","volume":"31","author":"MR Sullivan","year":"2019","unstructured":"Sullivan MR, Yao W, Gibb BC (2019) The thermodynamics of guest complexation to octa-acid and tetra-endo-methyl octa-acid: reference data for the sixth statistical assessment of modeling of proteins and ligands (SAMPL6). Supramol Chem 31(3):184\u2013189","journal-title":"Supramol Chem"},{"issue":"32","key":"290_CR114","doi-asserted-by":"crossref","first-page":"10235","DOI":"10.1021\/jp102971x","volume":"114","author":"A Pohorille","year":"2010","unstructured":"Pohorille A, Jarzynski C, Chipot C (2010) Good practices in free-energy calculations. J Phys Chem B 114(32):10235\u201310253","journal-title":"J Phys Chem B"},{"key":"290_CR115","doi-asserted-by":"crossref","unstructured":"Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM (2018) Best practices for quantification of uncertainty and sampling quality in molecular simulations [Article v1. 0]. Living J Comput Mol Sci. 1(1)","DOI":"10.33011\/livecoms.1.1.5067"},{"issue":"6","key":"290_CR116","doi-asserted-by":"crossref","first-page":"2867","DOI":"10.1021\/acs.jctc.7b01143","volume":"14","author":"AP Bhati","year":"2018","unstructured":"Bhati AP, Wan S, Hu Y, Sherborne B, Coveney PV (2018) Uncertainty quantification in alchemical free energy methods. J Chem Theory Comput 14(6):2867\u20132880","journal-title":"J Chem Theory Comput"},{"key":"290_CR117","unstructured":"Balasubramanian V, Jensen T, Turilli M, Kasson P, Shirts M, Jha S (2018) Adaptive ensemble biomolecular simulations at scale. arXiv:180404736"},{"issue":"6","key":"290_CR118","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1073\/pnas.1114017109","volume":"109","author":"L Wang","year":"2012","unstructured":"Wang L, Berne B, Friesner RA (2012) On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proc Natl Acad Sci 109(6):1937\u20131942","journal-title":"Proc Natl Acad Sci"},{"issue":"43","key":"290_CR119","doi-asserted-by":"crossref","first-page":"1831","DOI":"10.21105\/joss.01831","volume":"4","author":"L Hedges","year":"2019","unstructured":"Hedges L, Mey A, Laughton C, Gervasio F, Mulholland A, Woods C, Michel J (2019) BioSimSpace: an interoperable Python framework for biomolecular simulation. J Open Source Software 4(43):1831","journal-title":"Journal of Open Source Software"},{"key":"290_CR120","doi-asserted-by":"crossref","unstructured":"Dakka J, Turilli M, Wright DW, Zasada SJ, Balasubramanian V, Wan S, Coveney PV, Jha S (2018) High-throughput binding affinity calculations at extreme scales. BMC Bioinformatics 19(S18)","DOI":"10.1186\/s12859-018-2506-6"},{"issue":"12","key":"290_CR121","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s10822-007-9133-z","volume":"21","author":"JC Shelley","year":"2007","unstructured":"Shelley JC, Cholleti A, Frye LL, Greenwood JR, Timlin MR, Uchimaya M (2007) Epik: a software program for pK a prediction and protonation state generation for drug-like molecules. J Comput Aided Mol Des 21(12):681\u2013691. https:\/\/doi.org\/10.1007\/s10822-007-9133-z","journal-title":"J Comput Aided Mol Des"},{"issue":"6\u20137","key":"290_CR122","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1007\/s10822-010-9349-1","volume":"24","author":"JR Greenwood","year":"2010","unstructured":"Greenwood JR, Calkins D, Sullivan AP, Shelley JC (2010) Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. J Comput Aided Mol Des 24(6\u20137):591\u2013604. https:\/\/doi.org\/10.1007\/s10822-010-9349-1","journal-title":"J Comput Aided Mol Des"},{"issue":"2","key":"290_CR123","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","volume":"25","author":"J Wang","year":"2006","unstructured":"Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 25(2):247\u2013260","journal-title":"J Mol Graph Model"},{"key":"290_CR124","volume-title":"AMBER 16","author":"D Case","year":"2016","unstructured":"Case D, Betz R, Cerutti D, Cheatham T III, Darden T, Duke R, Giese T, Gohlke H, Goetz A, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee T, LeGrand S, Li P, Lin C, Luchko T et al (2016) AMBER 16. University of California, San Francisco"},{"issue":"30","key":"290_CR125","doi-asserted-by":"crossref","first-page":"9020","DOI":"10.1021\/jp8001614","volume":"112","author":"IS Joung","year":"2008","unstructured":"Joung IS, Cheatham TE III (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112(30):9020\u20139041","journal-title":"J Phys Chem B"},{"key":"290_CR126","doi-asserted-by":"publisher","unstructured":"Chodera J, Rizzi A, Naden L, Beauchamp K, Grinaway P, Fass J, Rustenburg B, Ross GA, Simmonett A, Swenson DWH (2018) choderalab\/openmmtools: 0.14.0: exact treatment of alchemical PME electrostatics, water cluster test system, optimizations. https:\/\/doi.org\/10.5281\/zenodo.1161149","DOI":"10.5281\/zenodo.1161149"},{"issue":"8","key":"290_CR127","doi-asserted-by":"publisher","first-page":"1528","DOI":"10.1016\/j.bpj.2015.08.015","volume":"109","author":"RT McGibbon","year":"2015","unstructured":"McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hern\u00e1ndez CX, Schwantes CR, Wang LP, Lane TJ, Pande VS (2015) MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Biophys J 109(8):1528\u20131532. https:\/\/doi.org\/10.1016\/j.bpj.2015.08.015","journal-title":"Biophys J"},{"issue":"14","key":"290_CR128","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1103\/PhysRevLett.45.1196","volume":"45","author":"M Parrinello","year":"1980","unstructured":"Parrinello M, Rahman A (1980) Crystal structure and pair potentials: a molecular-dynamics study. Phys Rev Lett 45(14):1196","journal-title":"Phys Rev Lett"},{"issue":"5","key":"290_CR129","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1002\/jcc.23804","volume":"36","author":"V Gapsys","year":"2015","unstructured":"Gapsys V, Michielssens S, Seeliger D, de Groot BL (2015) pmx: automated protein structure and topology generation for alchemical perturbations. J Comput Chem 36(5):348\u2013354","journal-title":"J Comput Chem"},{"issue":"2","key":"290_CR130","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/0021-9991(76)90078-4","volume":"22","author":"CH Bennett","year":"1976","unstructured":"Bennett CH (1976) Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys 22(2):245\u2013268. https:\/\/doi.org\/10.1016\/0021-9991(76)90078-4","journal-title":"J Comput Phys"},{"issue":"14","key":"290_CR131","doi-asserted-by":"crossref","first-page":"140601","DOI":"10.1103\/PhysRevLett.91.140601","volume":"91","author":"MR Shirts","year":"2003","unstructured":"Shirts MR, Bair E, Hooker G, Pande VS (2003) Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Phys Rev Lett 91(14):140601","journal-title":"Phys Rev Lett"},{"issue":"11","key":"290_CR132","doi-asserted-by":"crossref","first-page":"4613","DOI":"10.1063\/1.470648","volume":"103","author":"SE Feller","year":"1995","unstructured":"Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103(11):4613\u20134621","journal-title":"J Chem Phys"},{"issue":"12","key":"290_CR133","doi-asserted-by":"crossref","first-page":"124901","DOI":"10.1063\/1.1867374","volume":"122","author":"AF Jakobsen","year":"2005","unstructured":"Jakobsen AF (2005) Constant-pressure and constant-surface tension simulations in dissipative particle dynamics. J Chem Phys 122(12):124901","journal-title":"J Chem Phys"},{"issue":"8","key":"290_CR134","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.1021\/ct300242f","volume":"8","author":"P Liu","year":"2012","unstructured":"Liu P, Dehez F, Cai W, Chipot C (2012) A toolkit for the analysis of free-energy perturbation calculations. J Chem Theory Comput 8(8):2606\u20132616","journal-title":"J Chem Theory Comput"},{"issue":"4","key":"290_CR135","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1021\/acs.jctc.5b00784","volume":"12","author":"JD Chodera","year":"2016","unstructured":"Chodera JD (2016) A simple method for automated equilibration detection in molecular simulations. J Chem Theory Comput 12(4):1799\u20131805","journal-title":"J Chem Theory Comput"},{"key":"290_CR136","doi-asserted-by":"publisher","unstructured":"Sheppard K, Khrapov S, Lipt\u00e1k G, Capellini R (2018) esvhd, Hugle, JPN, RENE-CORAIL X, Rose ME, jbrockmendel, bashtage\/arch: Release 4.7. 2018. https:\/\/doi.org\/10.5281\/zenodo.2240590","DOI":"10.5281\/zenodo.2240590"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-020-00290-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-020-00290-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-020-00290-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T14:35:56Z","timestamp":1722350156000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-020-00290-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,27]]},"references-count":136,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2020,5]]}},"alternative-id":["290"],"URL":"https:\/\/doi.org\/10.1007\/s10822-020-00290-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/795005","asserted-by":"object"}]},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,27]]},"assertion":[{"value":"11 October 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 January 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 January 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}