{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:27:34Z","timestamp":1772119654079,"version":"3.50.1"},"reference-count":121,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T00:00:00Z","timestamp":1597017600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T00:00:00Z","timestamp":1597017600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","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":[[2021,1]]},"DOI":"10.1007\/s10822-020-00335-9","type":"journal-article","created":{"date-parts":[[2020,8,9]],"date-time":"2020-08-09T22:02:25Z","timestamp":1597010545000},"page":"105-115","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["SAMPL7 TrimerTrip host\u2013guest binding poses and binding affinities from spherical-coordinates-biased simulations"],"prefix":"10.1007","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8311-7797","authenticated-orcid":false,"given":"Zhaoxi","family":"Sun","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,8,10]]},"reference":[{"key":"335_CR1","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1126\/science.1096361","volume":"303","author":"WL Jorgensen","year":"2004","unstructured":"Jorgensen WL (2004) The many roles of computation in drug discovery. Science 303:1813\u20131818","journal-title":"Science"},{"key":"335_CR2","doi-asserted-by":"crossref","first-page":"767","DOI":"10.2174\/092986710790514453","volume":"17","author":"T Steinbrecher","year":"2010","unstructured":"Steinbrecher T, Labahn A (2010) Towards accurate free energy calculations in ligand protein-binding studies. Curr Med Chem 17:767\u2013785","journal-title":"Curr Med Chem"},{"key":"335_CR3","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1021\/ct900587b","volume":"6","author":"D Shivakumar","year":"2010","unstructured":"Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W (2010) Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput 6:1509\u20131519","journal-title":"J Chem Theory Comput"},{"key":"335_CR4","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1214\/ss\/1028905934","volume":"13","author":"A Gelman","year":"1998","unstructured":"Gelman A (1998) Meng X-L, Simulating normalizing constants: from importance sampling to bridge sampling to path sampling. Stat Sci 13:163\u2013185","journal-title":"Stat Sci"},{"key":"335_CR5","doi-asserted-by":"crossref","first-page":"124124","DOI":"10.1063\/1.4978893","volume":"146","author":"Z Sun","year":"2017","unstructured":"Sun Z, Yan YN, Yang M, Zhang JZ (2017) Interaction entropy for Protein-Protein binding. J Chem Phys 146:124124","journal-title":"J Chem Phys"},{"key":"335_CR6","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 114:10235\u201310253","journal-title":"J Phys Chem B"},{"key":"335_CR7","doi-asserted-by":"crossref","first-page":"164103","DOI":"10.1063\/1.3701766","volume":"136","author":"I Kim","year":"2012","unstructured":"Kim I, Allen TW (2012) Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space. J Chem Phys 136:164103\u2013164103","journal-title":"J Chem Phys"},{"key":"335_CR8","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 122:144107\u2013144107","journal-title":"J Chem Phys"},{"key":"335_CR9","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1002\/jcc.21712","volume":"32","author":"S Bruckner","year":"2011","unstructured":"Bruckner S, Boresch S (2011) Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration. J Comput Chem 32:1320\u20131333","journal-title":"J Comput Chem"},{"key":"335_CR10","doi-asserted-by":"crossref","first-page":"3701","DOI":"10.1080\/00268970601074421","volume":"104","author":"DA Kofke","year":"2006","unstructured":"Kofke DA (2006) On the sampling requirements for exponential-work free-energy calculations. Mol Phys 104:3701\u20133708","journal-title":"Mol Phys"},{"key":"335_CR11","doi-asserted-by":"crossref","first-page":"14188","DOI":"10.1021\/j100038a062","volume":"99","author":"G Hummer","year":"1995","unstructured":"Hummer G, Pratt LR, Garcia AE (1995) Hydration free energy of water. J Phys Chem 99:14188\u201314194","journal-title":"J Phys Chem"},{"key":"335_CR12","doi-asserted-by":"crossref","first-page":"011113","DOI":"10.1103\/PhysRevE.79.011113","volume":"79","author":"A Hahn","year":"2009","unstructured":"Hahn A, Then H (2009) Using bijective maps to improve free-energy estimates. Phys Rev E 79:011113","journal-title":"Phys Rev E"},{"key":"335_CR13","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.cplett.2017.07.003","volume":"684","author":"Z Sun","year":"2017","unstructured":"Sun Z, Wang X, Zhang JZH (2017) Protonation-dependent base flipping in the catalytic triad of a small RNA. Chem Phys Lett 684:239\u2013244","journal-title":"Chem Phys Lett"},{"key":"335_CR14","doi-asserted-by":"crossref","first-page":"035011","DOI":"10.1088\/0143-0807\/35\/3\/035011","volume":"35","author":"D Villamaina","year":"2014","unstructured":"Villamaina D, Trizac E (2014) Thinking outside the box: fluctuations and finite size effects. Eur J Phys 35:035011","journal-title":"Eur J Phys"},{"key":"335_CR15","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1140\/epje\/i2018-11675-x","volume":"41","author":"M Heidari","year":"2018","unstructured":"Heidari M, Cortes-Huerto R, Kremer K, Potestio R (2018) Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations. Eur Phys J E 41:64","journal-title":"Eur Phys J E"},{"key":"335_CR16","doi-asserted-by":"crossref","first-page":"4635","DOI":"10.1063\/1.474824","volume":"107","author":"F Rom\u00e1n","year":"1997","unstructured":"Rom\u00e1n F, White J, Velasco S (1997) Fluctuations in an equilibrium hard-disk fluid: explicit size effects. J Chem Phys 107:4635\u20134641","journal-title":"J Chem Phys"},{"key":"335_CR17","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1103\/PhysRev.122.1675","volume":"122","author":"J Lebowitz","year":"1961","unstructured":"Lebowitz J, Percus J (1961) Long-range correlations in a closed system with applications to nonuniform fluids. Phys Rev 122:1675","journal-title":"Phys Rev"},{"key":"335_CR18","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1103\/PhysRevE.53.2382","volume":"53","author":"J Salacuse","year":"1996","unstructured":"Salacuse J, Denton A, Egelstaff P (1996) Finite-size effects in molecular dynamics simulations: static structure factor and compressibility. I. Theoretical method. Phys Rev E 53:2382","journal-title":"Phys Rev E"},{"key":"335_CR19","doi-asserted-by":"crossref","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 (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545\u20131614","journal-title":"J Comput Chem"},{"key":"335_CR20","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 26:1781\u20131802","journal-title":"J Comput Chem"},{"key":"335_CR21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/jcph.1995.1039","volume":"117","author":"S Plimpton","year":"1995","unstructured":"Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys 117:1\u201319","journal-title":"J Comput Phys"},{"key":"335_CR22","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1021\/ja011973h","volume":"124","author":"SET And","year":"2002","unstructured":"And SET, Smithrud DB (2002) Carboxylates stacked over aromatic rings promote salt bridge formation in water. J Am Chem Soc 124:442","journal-title":"J Am Chem Soc"},{"key":"335_CR23","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1073\/pnas.0406847102","volume":"102","author":"OS Makin","year":"2005","unstructured":"Makin OS, Atkins E, Sikorski P, Johansson J, Serpell LC (2005) Molecular basis for amyloid fibril formation and stability. Proc Natl Acad Sci USA 102:315\u2013320","journal-title":"Proc Natl Acad Sci USA"},{"key":"335_CR24","doi-asserted-by":"crossref","first-page":"13262","DOI":"10.1021\/acs.jpcb.5b07248","volume":"119","author":"P Rani","year":"2015","unstructured":"Rani P, Biswas P (2015) Diffusion of hydration water around intrinsically disordered proteins. J Phys Chem B 119:13262\u201313270","journal-title":"J Phys Chem B"},{"key":"335_CR25","doi-asserted-by":"crossref","first-page":"14622","DOI":"10.1021\/acs.jpcb.5b08619","volume":"119","author":"Z GlH","year":"2015","unstructured":"GlH Z, RB B, J M (2015) Sequence-and temperature-dependent properties of unfolded and disordered proteins from atomistic simulations. J Phys Chem B 119:14622\u201314630","journal-title":"J Phys Chem B"},{"key":"335_CR26","doi-asserted-by":"crossref","first-page":"1462","DOI":"10.1016\/j.bpj.2012.02.024","volume":"102","author":"RB Best","year":"2012","unstructured":"Best RB, de Sancho D, Mittal J (2012) Residue-specific \u03b1-helix propensities from molecular simulation. Biophys J 102:1462\u20131467","journal-title":"Biophys J"},{"key":"335_CR27","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1021\/acs.jpcb.6b08541","volume":"121","author":"M Makowski","year":"2017","unstructured":"Makowski M, Liwo A, Scheraga HA (2017) Simple Physics-based analytical formulas for the potentials of mean force of the interaction of amino acid side chains in water. VII. Charged\u2013hydrophobic\/polar and polar\u2013hydrophobic\/polar side chains. J Phys Chem B 121:379\u2013390","journal-title":"J Phys Chem B"},{"key":"335_CR28","doi-asserted-by":"crossref","first-page":"6059","DOI":"10.1021\/bi00238a033","volume":"30","author":"DJ Tobias","year":"1991","unstructured":"Tobias DJ, Brooks CL III (1991) Thermodynamics and mechanism of. alpha. helix initiation in alanine and valine peptides. Biochem 30:6059\u20136070","journal-title":"Biochem"},{"key":"335_CR29","doi-asserted-by":"crossref","first-page":"4850","DOI":"10.1021\/acs.jpclett.5b02164","volume":"6","author":"PS Hudson","year":"2015","unstructured":"Hudson PS, Woodcock HL, Boresch S (2015) Use of nonequilibrium work methods to compute free energy differences between molecular mechanical and quantum mechanical representations of molecular systems. J Phys Chem Lett 6:4850\u20134856","journal-title":"J Phys Chem Lett"},{"key":"335_CR30","doi-asserted-by":"crossref","first-page":"8120","DOI":"10.1021\/jp801688p","volume":"112","author":"FJ Mart\u00ednezveracoechea","year":"2008","unstructured":"Mart\u00ednezveracoechea FJ, Escobedo FA (2008) Variance minimization of free energy estimates from optimized expanded ensembles. J Phys Chem B 112:8120\u20138128","journal-title":"J Phys Chem B"},{"key":"335_CR31","unstructured":"Wang X, Sun Z (2018) A theoretical interpretation of variance-based convergence citeria in perturbation-based theories. ArXiv Preprint. arXiv:1803.03123"},{"key":"335_CR32","doi-asserted-by":"crossref","first-page":"6672","DOI":"10.1039\/C8CP07012A","volume":"21","author":"X Wang","year":"2019","unstructured":"Wang X, He Q, Sun Z (2019) BAR-based multi-dimensional nonequilibrium pulling for indirect construction of a QM\/MM free energy landscape. Phys Chem Chem Phys 21:6672\u20136688","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR33","doi-asserted-by":"crossref","first-page":"21942","DOI":"10.1039\/C9CP04113C","volume":"21","author":"Z Sun","year":"2019","unstructured":"Sun Z (2019) BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM\/MM free energy landscapes: from semi-empirical to ab initio. Phys Chem Chem Phys 21:21942\u201321959","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR34","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1002\/jcc.25784","volume":"40","author":"X Wang","year":"2019","unstructured":"Wang X, Xingzhao T, Boming D, John ZHZ, Sun Z (2019) BAR-based optimum adaptive steered MD for configurational sampling. J Comput Chem 40:1270\u20131289","journal-title":"J Comput Chem"},{"key":"335_CR35","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1002\/wcms.66","volume":"1","author":"J K\u00e4stner","year":"2011","unstructured":"K\u00e4stner J (2011) Umbrella sampling. Wiley Interdisip Rev Comput Mol Sci 1:932\u2013942","journal-title":"Wiley Interdisip Rev Comput Mol Sci"},{"key":"335_CR36","doi-asserted-by":"crossref","first-page":"14923","DOI":"10.1039\/C9CP01989H","volume":"21","author":"Z Sun","year":"2019","unstructured":"Sun Z, Wang X, Zhang JZH, He Q (2019) Sulfur-substitution-induced base flipping in the DNA duplex. Phys Chem Chem Phys 21:14923\u201314940","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR37","doi-asserted-by":"publisher","DOI":"10.26434\/chemrxiv.11483178.v1","author":"Z Sun","year":"2020","unstructured":"Sun Z, Zhang JZ (2020) Thermodynamic insights of base flipping in TNA duplex: force fields, salt concentrations, and free energy simulation methods. ChemRxiv Preprint. https:\/\/doi.org\/10.26434\/chemrxiv.11483178.v1","journal-title":"ChemRxiv Preprint"},{"key":"335_CR38","doi-asserted-by":"crossref","first-page":"9058","DOI":"10.1063\/1.1472510","volume":"116","author":"H Fukunishi","year":"2002","unstructured":"Fukunishi H, Watanabe O, Takada S (2002) On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J Chem Phys 116:9058\u20139067","journal-title":"J Chem Phys"},{"key":"335_CR39","doi-asserted-by":"crossref","first-page":"3420","DOI":"10.1002\/prot.23176","volume":"79","author":"SG Itoh","year":"2011","unstructured":"Itoh SG, Damjanovic A, Brooks BR (2011) pH replica-exchange method based on discrete protonation states. Proteins 79:3420\u20133436","journal-title":"Proteins"},{"key":"335_CR40","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1021\/ct050196z","volume":"2","author":"A Okur","year":"2006","unstructured":"Okur A, Wickstrom L, Layten M, Geney R, Song K, Hornak V, Simmerling C (2006) Improved efficiency of replica exchange simulations through use of a hybrid explicit\/implicit solvation model. J Chem Theory Comput 2:420","journal-title":"J Chem Theory Comput"},{"key":"335_CR41","doi-asserted-by":"crossref","first-page":"6981","DOI":"10.1021\/bi500695g","volume":"53","author":"T Gurry","year":"2014","unstructured":"Gurry T, Stultz CM (2014) Mechanism of amyloid-\u03b2 fibril elongation. Biochem 53:6981\u20136991","journal-title":"Biochem"},{"key":"335_CR42","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0009-2614(99)01123-9","volume":"314","author":"Y Sugita","year":"1999","unstructured":"Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314:141\u2013151","journal-title":"Chem Phys Lett"},{"key":"335_CR43","doi-asserted-by":"crossref","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 113:6042\u20136051","journal-title":"J Chem Phys"},{"key":"335_CR44","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1021\/acs.jcim.7b00177","volume":"57","author":"Z Sun","year":"2017","unstructured":"Sun Z, Wang X, Song J (2017) Extensive assessment of various computational methods for Aspartate\u2019s pKa Shift. J Chem Inf Model 57:1621\u20131639","journal-title":"J Chem Inf Model"},{"key":"335_CR45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2091-7-18","volume":"7","author":"MN Davies","year":"2006","unstructured":"Davies MN, Toseland CP, Moss DS, Flower DR (2006) Benchmarking pKa prediction. BMC Biochemistry 7:1\u201312","journal-title":"BMC Biochemistry"},{"key":"335_CR46","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1021\/ct8000014","volume":"4","author":"CL Stanton","year":"2008","unstructured":"Stanton CL, Houk KN (2008) Benchmarking pKa Prediction methods for Residues in proteins. J Chem Theory Comput 4:951\u2013966","journal-title":"J Chem Theory Comput"},{"key":"335_CR47","doi-asserted-by":"crossref","first-page":"3888","DOI":"10.1529\/biophysj.104.055996","volume":"88","author":"G Archontis","year":"2005","unstructured":"Archontis G, Simonson T (2005) Proton binding to proteins: a free-energy component analysis using a dielectric continuum model. Biophys J 88:3888\u20133904","journal-title":"Biophys J"},{"key":"335_CR48","first-page":"1999","volume":"363","author":"PW Fowler","year":"2005","unstructured":"Fowler PW, Jha S, Coveney PV (2005) Grid-based steered thermodynamic integration accelerates the calculation of binding free energies. Philos Trans R Soc Math Phys Eng Sci 363:1999\u20132015","journal-title":"Philos Trans R Soc Math Phys Eng Sci"},{"key":"335_CR49","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1080\/08927020211973","volume":"28","author":"JW Pitera","year":"2002","unstructured":"Pitera JW, van Gunsteren WF (2002) A comparison of non-bonded scaling approaches for free energy calculations. Mol Simul 28:45\u201365","journal-title":"Mol Simul"},{"key":"335_CR50","doi-asserted-by":"crossref","first-page":"15005","DOI":"10.1039\/C7CP01561E","volume":"19","author":"ZX Sun","year":"2017","unstructured":"Sun ZX, Wang XH, Zhang JZH (2017) BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation. Phys Chem Chem Phys 19:15005\u201315020","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR51","doi-asserted-by":"crossref","first-page":"2009","DOI":"10.1039\/C7CP07573A","volume":"20","author":"X Wang","year":"2018","unstructured":"Wang X, Tu X, Zhang JZH, Sun Z (2018) BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification. Phys Chem Chem Phys 20:2009\u20132021","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR52","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/0009-2614(90)80029-D","volume":"166","author":"MJ Frisch","year":"1990","unstructured":"Frisch MJ, Head-Gordon M, Pople JA (1990) A direct MP2 gradient method. Chem Phys Lett 166:275\u2013280","journal-title":"Chem Phys Lett"},{"key":"335_CR53","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/0009-2614(88)85250-3","volume":"153","author":"M Head-Gordon","year":"1988","unstructured":"Head-Gordon M, Pople JA, Frisch MJ (1988) MP2 energy evaluation by direct methods. Chem Phys Lett 153:503\u2013506","journal-title":"Chem Phys Lett"},{"key":"335_CR54","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/S0009-2614(97)00207-8","volume":"268","author":"RH Hertwig","year":"1997","unstructured":"Hertwig RH, Koch W (1997) On the parameterization of the local correlation functional. What is Becke-3-LYP? Chem Phys Lett 268:345\u2013351","journal-title":"Chem Phys Lett"},{"key":"335_CR55","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/S0009-2614(99)00874-X","volume":"313","author":"K Kitaura","year":"1999","unstructured":"Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M (1999) Fragment molecular orbital method: an approximate computational method for large molecules. Chem Phys Lett 313:701\u2013706","journal-title":"Chem Phys Lett"},{"key":"335_CR56","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1002\/jcc.540161106","volume":"16","author":"P Cieplak","year":"1995","unstructured":"Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J Comput Chem 16:1357\u20131377","journal-title":"J Comput Chem"},{"key":"335_CR57","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1002\/jcc.10156","volume":"24","author":"T Vreven","year":"2003","unstructured":"Vreven T, Morokuma K, Farkas \u00d6, Schlegel HB, Frisch MJ (2003) Geometry optimization with QM\/MM, ONIOM, and other combined methods. I. Microiterations and constraints. J Comput Chem 24:760\u2013769","journal-title":"J Comput Chem"},{"key":"335_CR58","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1007\/s00894-007-0233-4","volume":"13","author":"JJ Stewart","year":"2007","unstructured":"Stewart JJ (2007) Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model 13:1173\u20131213","journal-title":"J Mol Model"},{"key":"335_CR59","doi-asserted-by":"crossref","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","volume":"92","author":"A P\u00e9rez","year":"2007","unstructured":"P\u00e9rez A, March\u00e1n I, Svozil D, Sponer J, Cheatham TE III, Laughton CA, Orozco M (2007) Refinement of the AMBER force field for nucleic acids: improving the description of \u03b1\/\u03b3 conformers. Biophys J 92:3817\u20133829","journal-title":"Biophys J"},{"key":"335_CR60","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","volume":"65","author":"V Hornak","year":"2006","unstructured":"Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712\u2013725","journal-title":"Proteins"},{"key":"335_CR61","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"JA Maier","year":"2015","unstructured":"Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696\u20133713","journal-title":"J Chem Theory Comput"},{"key":"335_CR62","doi-asserted-by":"crossref","first-page":"8910","DOI":"10.1063\/1.481505","volume":"112","author":"MW Mahoney","year":"2000","unstructured":"Mahoney MW, Jorgensen WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys 112:8910\u20138922","journal-title":"J Chem Phys"},{"key":"335_CR63","doi-asserted-by":"crossref","first-page":"L07","DOI":"10.1529\/biophysj.108.132696","volume":"95","author":"RB Best","year":"2008","unstructured":"Best RB, Buchete N-V, Hummer G (2008) Are current molecular dynamics force fields too helical? Biophys J 95:L07\u2013L09","journal-title":"Biophys J"},{"key":"335_CR64","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.cplett.2017.08.059","volume":"687","author":"Z Sun","year":"2017","unstructured":"Sun Z, Zhu T, Wang X, Mei Y, Zhang JZ (2017) Optimization of convergence criteria for fragmentation methods. Chem Phys Lett 687:163\u2013170","journal-title":"Chem Phys Lett"},{"key":"335_CR65","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1021\/cr500606e","volume":"115","author":"K Raghavachari","year":"2015","unstructured":"Raghavachari K, Saha A (2015) Accurate composite and fragment-based quantum chemical models for large molecules. Chem Rev 115:5643\u20135677","journal-title":"Chem Rev"},{"key":"335_CR66","doi-asserted-by":"crossref","first-page":"5607","DOI":"10.1021\/cr500455b","volume":"115","author":"MA Collins","year":"2015","unstructured":"Collins MA, Bettens RP (2015) Energy-based molecular fragmentation methods. Chem Rev 115:5607\u20135642","journal-title":"Chem Rev"},{"key":"335_CR67","doi-asserted-by":"crossref","first-page":"2739","DOI":"10.1021\/ar500079b","volume":"47","author":"N Sahu","year":"2014","unstructured":"Sahu N, Gadre SR (2014) Molecular tailoring approach: a route for ab initio treatment of large clusters. Acc Chem Res 47:2739\u20132747","journal-title":"Acc Chem Res"},{"key":"335_CR68","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1002\/jcc.23905","volume":"36","author":"WJ Allen","year":"2015","unstructured":"Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC (2015) DOCK 6: Impact of new features and current docking performance. J Comput Chem 36:1132\u20131156","journal-title":"J Comput Chem"},{"key":"335_CR69","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.cbi.2006.12.006","volume":"171","author":"I Kapetanovic","year":"2008","unstructured":"Kapetanovic I (2008) Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chem Biol Interact 171:165\u2013176","journal-title":"Chem Biol Interact"},{"key":"335_CR70","doi-asserted-by":"crossref","first-page":"6237","DOI":"10.1021\/jm800562d","volume":"51","author":"P Cozzini","year":"2008","unstructured":"Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, Emerson A, Fanelli F, Gohlke H, Kuhn LA, Morris GM (2008) Target flexibility: an emerging consideration in drug discovery and design. J Med Chem 51:6237\u20136255","journal-title":"J Med Chem"},{"key":"335_CR71","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/prot.10115","volume":"47","author":"I Halperin","year":"2002","unstructured":"Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47:409\u2013443","journal-title":"Proteins"},{"key":"335_CR72","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1002\/(SICI)1097-0134(19990101)34:1<4::AID-PROT2>3.0.CO;2-6","volume":"34","author":"BK Shoichet","year":"1999","unstructured":"Shoichet BK, Leach AR, Kuntz ID (1999) Ligand solvation in molecular docking. Proteins 34:4","journal-title":"Proteins"},{"key":"335_CR73","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/prot.22058","volume":"73","author":"CA Sotriffer","year":"2008","unstructured":"Sotriffer CA, Sanschagrin P, Matter H, Klebe G (2008) SFCscore: scoring functions for affinity prediction of protein\u2013ligand complexes. Proteins 73:395\u2013419","journal-title":"Proteins"},{"key":"335_CR74","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.jmgm.2004.11.007","volume":"23","author":"A Krammer","year":"2005","unstructured":"Krammer A, Kirchhoff PD, Jiang X, Venkatachalam C, Waldman M (2005) LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 23:395\u2013407","journal-title":"J Mol Graph Model"},{"key":"335_CR75","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S1093-3263(01)00125-5","volume":"20","author":"RD Clark","year":"2002","unstructured":"Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB (2002) Consensus scoring for ligand\/protein interactions. J Mol Graph Model 20:281\u2013295","journal-title":"J Mol Graph Model"},{"key":"335_CR76","doi-asserted-by":"crossref","first-page":"5912","DOI":"10.1021\/jm050362n","volume":"49","author":"GL Warren","year":"2006","unstructured":"Warren GL, Andrews CW, Capelli A-M, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49:5912\u20135931","journal-title":"J Med Chem"},{"key":"335_CR77","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1021\/acs.jcim.7b00017","volume":"57","author":"Y Yan","year":"2017","unstructured":"Yan Y, Wang W, Sun Z, Zhang JZ, Ji C (2017) Protein\u2013ligand empirical interaction components for virtual screening. J Chem Inf Model 57:1793\u20131806","journal-title":"J Chem Inf Model"},{"key":"335_CR78","doi-asserted-by":"crossref","first-page":"7865","DOI":"10.1016\/j.bmc.2007.08.019","volume":"15","author":"AM Ferrari","year":"2007","unstructured":"Ferrari AM, Degliesposti G, Sgobba M, Rastelli G (2007) Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. Biorg Med Chem 15:7865\u20137877","journal-title":"Biorg Med Chem"},{"key":"335_CR79","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1002\/jcc.10379","volume":"25","author":"H Gohlke","year":"2004","unstructured":"Gohlke H, Case DA (2004) Converging free energy estimates: MM-PB (GB) SA studies on the protein\u2013protein complex Ras-Raf. J Comput Chem 25:238\u2013250","journal-title":"J Comput Chem"},{"key":"335_CR80","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S0959-440X(94)90321-2","volume":"4","author":"DA Case","year":"2010","unstructured":"Case DA (2010) Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4:285\u2013290","journal-title":"Curr Opin Struct Biol"},{"key":"335_CR81","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1021\/ci200033n","volume":"51","author":"C Rapp","year":"2011","unstructured":"Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP (2011) A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. J Chem Inf Model 51:2082\u20132089","journal-title":"J Chem Inf Model"},{"key":"335_CR82","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1063\/1.442716","volume":"76","author":"WC Swope","year":"1982","unstructured":"Swope WC (1982) A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters. J Chem Phys 76:637","journal-title":"J Chem Phys"},{"key":"335_CR83","doi-asserted-by":"crossref","first-page":"034114","DOI":"10.1063\/1.3607597","volume":"135","author":"TT Pham","year":"2011","unstructured":"Pham TT, Shirts MR (2011) Identifying low variance pathways for free energy calculations of molecular transformations in solution phase. J Chem Phys 135:034114","journal-title":"J Chem Phys"},{"key":"335_CR84","doi-asserted-by":"crossref","first-page":"1924","DOI":"10.1021\/acs.jctc.6b01192","volume":"13","author":"P Procacci","year":"2017","unstructured":"Procacci P, Chelli R (2017) Statistical mechanics of ligand-receptor noncovalent association, revisited: binding site and standard state volumes in Modern Alchemical theories. J Chem Theory Comput 13:1924\u20131933","journal-title":"J Chem Theory Comput"},{"key":"335_CR85","doi-asserted-by":"crossref","first-page":"7544","DOI":"10.1039\/C9CP00070D","volume":"21","author":"X Wang","year":"2019","unstructured":"Wang X, Sun Z (2019) Understanding PIM-1 kinase inhibitor interactions with free energy simulation. Phys Chem Chem Phys 21:7544\u20137558","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR86","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.jmgm.2019.05.011","volume":"91","author":"Z Sun","year":"2019","unstructured":"Sun Z, Wang X, Zhao Q, Zhu T (2019) Understanding aldose reductase-inhibitors interactions with free energy simulation. J Mol Graph Model 91:10\u201321","journal-title":"J Mol Graph Model"},{"key":"335_CR87","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cplett.2019.03.020","volume":"723","author":"Z Sun","year":"2019","unstructured":"Sun Z, Wang X, Zhang JZ (2019) Determination of binding affinities of 3-Hydroxy-3-methylglutaryl coenzyme a reductase inhibitors from free energy calculation. Chem Phys Lett 723:1\u201310","journal-title":"Chem Phys Lett"},{"key":"335_CR88","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1039\/C9CP05980F","volume":"22","author":"Z Sun","year":"2020","unstructured":"Sun Z, Wang X, Zhang JZ (2020) Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding. Phys Chem Chem Phys 22:1511\u20131524","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR89","doi-asserted-by":"crossref","first-page":"E2136","DOI":"10.1073\/pnas.1612627114","volume":"114","author":"F Moraca","year":"2017","unstructured":"Moraca F, Amato J, Ortuso F, Artese A, Pagano B, Novellino E, Alcaro S, Parrinello M, Limongelli V (2017) Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Proc Natl Acad Sci USA 114:E2136\u2013E2145","journal-title":"Proc Natl Acad Sci USA"},{"key":"335_CR90","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1146\/annurev-physchem-040215-112229","volume":"67","author":"O Valsson","year":"2016","unstructured":"Valsson O, Tiwary P, Parrinello M (2016) Enhancing important fluctuations: rare events and metadynamics from a conceptual viewpoint. Annu Rev Phys Chem 67:159","journal-title":"Annu Rev Phys Chem"},{"key":"335_CR91","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1073\/pnas.1424461112","volume":"112","author":"P Tiwary","year":"2015","unstructured":"Tiwary P, Limongelli V, Salvalaglio M, Parrinello M (2015) Kinetics of protein-ligand unbinding: predicting pathways, rates, and rate-limiting steps. Proc Natl Acad Sci USA 112:386\u2013391","journal-title":"Proc Natl Acad Sci USA"},{"key":"335_CR92","doi-asserted-by":"crossref","first-page":"5166","DOI":"10.1039\/B608269F","volume":"8","author":"N Huang","year":"2006","unstructured":"Huang N, Kalyanaraman C, Bernacki K, Jacobson MP (2006) Molecular mechanics methods for predicting protein\u2013ligand binding. Phys Chem Chem Phys 8:5166\u20135177","journal-title":"Phys Chem Chem Phys"},{"key":"335_CR93","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s10822-014-9718-2","volume":"28","author":"DL Mobley","year":"2014","unstructured":"Mobley DL, Wymer KL, Lim NM, Guthrie JP (2014) Blind prediction of solvation free energies from the SAMPL4 challenge. J Comput Aided Mol Des 28:135\u2013150","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR94","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 28:401\u2013415","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR95","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1007\/s10822-018-0153-7","volume":"32","author":"LF Song","year":"2018","unstructured":"Song LF, Bansal N, Zheng Z, Merz KM (2018) Detailed potential of mean force studies on host\u2013guest systems from the SAMPL6 challenge. J Comput Aided Mol Des 32:1013\u20131026","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR96","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 (2018) Overview of the SAMPL6 host\u2013guest binding affinity prediction challenge. J Comput Aided Mol Des 32:937\u2013963","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR97","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1007\/s10822-018-0151-9","volume":"32","author":"P Procacci","year":"2018","unstructured":"Procacci P, Guarrasi M, Guarnieri G (2018) SAMPL6 host\u2013guest blind predictions using a non equilibrium alchemical approach. J Comput Aided Mol Des 32:965\u2013982","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR98","doi-asserted-by":"crossref","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\u2013guest challenges. J Comput Aided Mol Des 32:1075\u20131086","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR99","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1039\/C9NJ05336K","volume":"44","author":"SZ Ndendjio","year":"2020","unstructured":"Ndendjio SZ, Liu W, Yvanez N, Meng Z, Zavalij PY, Isaacs L (2020) Triptycene walled glycoluril trimer: synthesis and recognition properties. New J Chem 44:338\u2013345","journal-title":"New J Chem"},{"key":"335_CR100","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1007\/s10822-018-0158-2","volume":"32","author":"O Caldararu","year":"2018","unstructured":"Caldararu O, Olsson MA, Ignjatovi\u0107 MM, Wang M, Ryde U (2018) Binding free energies in the SAMPL6 octa-acid host\u2013guest challenge calculated with MM and QM methods. J Comput Aided Mol Des 32:1027\u20131046","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR101","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 32:1097\u20131115","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR102","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"},{"key":"335_CR103","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1007\/s10822-020-00294-1","volume":"34","author":"Z Sun","year":"2020","unstructured":"Sun Z, He Q, Li X, Zhu Z (2020) SAMPL6 host\u2013guest binding affinities and binding poses from spherical-coordinates-biased simulations. J Comput Aided Mol Des 34:589\u2013600","journal-title":"J Comput Aided Mol Des"},{"key":"335_CR104","unstructured":"https:\/\/github.com\/samplchallenges\/SAMPL6."},{"key":"335_CR105","unstructured":"https:\/\/github.com\/samplchallenges\/SAMPL7\/tree\/master\/host_guest\/Isaacs_clip."},{"key":"335_CR106","doi-asserted-by":"crossref","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 23:1623\u20131641","journal-title":"J Comput Chem"},{"key":"335_CR107","doi-asserted-by":"crossref","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 25:1157\u20131173","journal-title":"J Comput Chem"},{"key":"335_CR108","doi-asserted-by":"crossref","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 79:926\u2013935","journal-title":"J Chem Phys"},{"key":"335_CR109","doi-asserted-by":"crossref","first-page":"10096","DOI":"10.1063\/1.1808117","volume":"121","author":"DJ Price","year":"2004","unstructured":"Price DJ, Brooks CL III (2004) A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys 121:10096\u201310103","journal-title":"J Chem Phys"},{"key":"335_CR110","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 112:9020\u20139041","journal-title":"J Phys Chem B"},{"key":"335_CR111","doi-asserted-by":"crossref","first-page":"13279","DOI":"10.1021\/jp902584c","volume":"113","author":"IS Joung","year":"2009","unstructured":"Joung IS, Cheatham TE (2009) Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters. J Phys Chem B 113:13279\u201313290","journal-title":"J Phys Chem B"},{"key":"335_CR112","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1002\/wcms.31","volume":"1","author":"A Barducci","year":"2011","unstructured":"Barducci A, Bonomi M, Parrinello M (2011) Metadynamics. Wiley Interdisip Rev Comput Mol Sci 1:826\u2013843","journal-title":"Wiley Interdisip Rev Comput Mol Sci"},{"key":"335_CR113","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 100:020603","journal-title":"Phys Rev Lett"},{"key":"335_CR114","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1021\/jp504920s","volume":"119","author":"P Tiwary","year":"2015","unstructured":"Tiwary P, Parrinello M (2015) A time-independent free energy estimator for metadynamics. J Phys Chem B 119:736\u2013742","journal-title":"J Phys Chem B"},{"key":"335_CR115","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"},{"key":"335_CR116","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.cpc.2013.09.018","volume":"185","author":"GA Tribello","year":"2014","unstructured":"Tribello GA, Bonomi M, Branduardi D, Camilloni C, Bussi G (2014) PLUMED 2: new feathers for an old bird. Comput Phys Commun 185:604\u2013613","journal-title":"Comput Phys Commun"},{"key":"335_CR117","first-page":"2384","volume":"126","author":"B Giovanni","year":"2007","unstructured":"Giovanni B, Davide D, Michele P (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:2384","journal-title":"J Chem Phys"},{"key":"335_CR118","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1080\/00268978300102851","volume":"50","author":"S Nos\u00e9","year":"1983","unstructured":"Nos\u00e9 S, Klein ML (1983) Constant pressure molecular dynamics for molecular systems. Mol Phys 50:1055\u20131076","journal-title":"Mol Phys"},{"key":"335_CR119","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","volume":"52","author":"M Parrinello","year":"1981","unstructured":"Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52:7182\u20137190","journal-title":"J Appl Phys"},{"key":"335_CR120","doi-asserted-by":"crossref","first-page":"8345","DOI":"10.1063\/1.465608","volume":"99","author":"DM York","year":"1993","unstructured":"York DM, Darden TA, Pedersen LG (1993) The Effect of Long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and Truncated list methods. J Chem Phys 99:8345\u20138348","journal-title":"J Chem Phys"},{"key":"335_CR121","doi-asserted-by":"crossref","first-page":"6811","DOI":"10.1063\/1.460259","volume":"94","author":"ME Tuckerman","year":"1991","unstructured":"Tuckerman ME, Berne BJ, Martyna GJ (1991) Molecular dynamics algorithm for multiple time scales: systems with long range forces. J Chem Phys 94:6811\u20136815","journal-title":"J Chem Phys"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-020-00335-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-020-00335-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-020-00335-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,9]],"date-time":"2021-08-09T19:12:38Z","timestamp":1628536358000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-020-00335-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,10]]},"references-count":121,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,1]]}},"alternative-id":["335"],"URL":"https:\/\/doi.org\/10.1007\/s10822-020-00335-9","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.12047103.v1","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.12047103.v2","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.12047103","asserted-by":"object"}]},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,8,10]]},"assertion":[{"value":"4 April 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 August 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 August 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"There are no conflicts of interest to declare.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}