{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T07:37:31Z","timestamp":1740123451726,"version":"3.37.3"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T00:00:00Z","timestamp":1475193600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T00:00:00Z","timestamp":1475193600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000050","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":[[2017,1]]},"DOI":"10.1007\/s10822-016-9965-5","type":"journal-article","created":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T11:18:13Z","timestamp":1475234293000},"page":"107-118","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Absolute binding free energies for octa-acids and guests in SAMPL5"],"prefix":"10.1007","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2236-0512","authenticated-orcid":false,"given":"Florentina","family":"Tofoleanu","sequence":"first","affiliation":[]},{"given":"Juyong","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Frank C.","family":"Pickard IV","sequence":"additional","affiliation":[]},{"given":"Gerhard","family":"K\u00f6nig","sequence":"additional","affiliation":[]},{"given":"Jing","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Minkyung","family":"Baek","sequence":"additional","affiliation":[]},{"given":"Chaok","family":"Seok","sequence":"additional","affiliation":[]},{"given":"Bernard R.","family":"Brooks","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,9,30]]},"reference":[{"key":"9965_CR1","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1021\/jp0764384","volume":"112","author":"DL Mobley","year":"2008","unstructured":"Mobley DL, Dill KA, Chodera JD (2008) Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B 112:938\u2013946","journal-title":"J Phys Chem B"},{"issue":"2","key":"9965_CR2","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1021\/ct800409d","volume":"5","author":"DL Mobley","year":"2009","unstructured":"Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA (2009) Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations. J Chem Theory Comput 5(2):350\u2013358","journal-title":"J Chem Theory Comput"},{"issue":"19","key":"9965_CR3","doi-asserted-by":"publisher","first-page":"6750","DOI":"10.1073\/pnas.0407404102","volume":"102","author":"C Oostenbrink","year":"2005","unstructured":"Oostenbrink C, van Gunsteren WF (2005) Free energies of ligand binding for structurally diverse compounds. Proc Natl Acad Sci USA 102(19):6750\u20136754","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"9965_CR4","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1016\/j.jmb.2007.06.002","volume":"371","author":"DL Mobley","year":"2007","unstructured":"Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA (2007) Predicting absolute ligand binding free energies to a simple model site. J Mol Biol 371(4):1118\u20131134","journal-title":"J Mol Biol"},{"issue":"5665","key":"9965_CR5","doi-asserted-by":"publisher","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(5665):1813\u20131818","journal-title":"Science"},{"key":"9965_CR6","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1002\/jcc.540160306","volume":"16","author":"DL Severance","year":"1995","unstructured":"Severance DL, Essex JW, Jorgensen WL (1995) Generalized alteration of structure and parameters: a new method for free-energy perturbations in systems containing flexible degrees of freedom. J Comput Chem 16:311\u2013327","journal-title":"J Comput Chem"},{"key":"9965_CR7","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 22:245\u2013268","journal-title":"J Comput Phys"},{"key":"9965_CR8","doi-asserted-by":"publisher","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 91:140601","journal-title":"Phys Rev Lett"},{"key":"9965_CR9","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1063\/1.1749657","volume":"3","author":"JG Kirkwood","year":"1935","unstructured":"Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3:300\u2013313","journal-title":"J Chem Phys"},{"key":"9965_CR10","doi-asserted-by":"publisher","first-page":"6825","DOI":"10.1073\/pnas.0409005102","volume":"102","author":"H-J Woo","year":"2005","unstructured":"Woo H-J, Roux B (2005) Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA 102:6825\u20136830","journal-title":"Proc Natl Acad Sci USA"},{"issue":"27","key":"9965_CR11","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"},{"key":"9965_CR12","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1021\/ct3008099","volume":"9","author":"JC Gumbart","year":"2013","unstructured":"Gumbart JC, Roux B, Chipot C (2013) Standard binding free energies from computer simulations: what is the best strategy? J Chem Theory Comput 9:794\u2013802","journal-title":"J Chem Theory Comput"},{"issue":"1","key":"9965_CR13","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1021\/ci300505n","volume":"53","author":"S Jo","year":"2013","unstructured":"Jo S, Jiang W, Lee HS, Roux B, Im W (2013) Charmm-gui ligand binder for absolute binding free energy calculations and its application. J Chem Inf Model 53(1):267\u2013277","journal-title":"J Chem Inf Model"},{"issue":"4","key":"9965_CR14","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1021\/jm070549+","volume":"51","author":"A Nicholls","year":"2008","unstructured":"Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS (2008) Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem 51(4):769\u2013779","journal-title":"J Med Chem"},{"issue":"14","key":"9965_CR15","doi-asserted-by":"publisher","first-page":"4501","DOI":"10.1021\/jp806724u","volume":"113","author":"JP Guthrie","year":"2009","unstructured":"Guthrie JP (2009) A blind challenge for computational solvation free energies: introduction and overview. J Phys Chem B 113(14):4501\u20134507. doi: 10.1021\/jp806724u","journal-title":"J Phys Chem B"},{"issue":"4","key":"9965_CR16","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s10822-010-9350-8","volume":"24","author":"MT Geballe","year":"2010","unstructured":"Geballe MT, Skillman AG, Nicholls A, Guthrie JP, Taylor PJ (2010) The SAMPL2 blind prediction challenge: introduction and overview. J Comput Aided Mol Des 24(4):259\u2013279","journal-title":"J Comput Aided Mol Des"},{"issue":"5","key":"9965_CR17","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1007\/s10822-012-9554-1","volume":"26","author":"HS Muddana","year":"2012","unstructured":"Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK (2012) Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des 26(5):475\u2013487. doi: 10.1007\/s10822-012-9554-1","journal-title":"J Comput Aided Mol Des"},{"issue":"4","key":"9965_CR18","doi-asserted-by":"publisher","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-guest blind prediction challenge: an overview. J Comput Aided Mol Des 28(4):305\u2013317","journal-title":"J Comput Aided Mol Des"},{"key":"9965_CR19","doi-asserted-by":"publisher","unstructured":"Yin J, Henriksen NM, Slochower DR, Chiu MW, Mobley DL, Gilson MK (2016) Overview of the SAMPL5 host-guest challenge: are we doing better? J Comput Aided Mol Des. doi: 10.1007\/s10822-016-9974-4","DOI":"10.1007\/s10822-016-9974-4"},{"issue":"3","key":"9965_CR20","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1007\/s10822-014-9720-8","volume":"28","author":"BA Ellingson","year":"2014","unstructured":"Ellingson BA, Geballe MT, Wlodek S, Bayly CI, Skillman AG, Nicholls A (2014) Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK. J Comput Aided Mol Des 28(3):289\u2013298","journal-title":"J Comput Aided Mol Des"},{"issue":"3","key":"9965_CR21","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/s10822-014-9727-1","volume":"28","author":"O Beckstein","year":"2014","unstructured":"Beckstein O, Fourrier A, Iorga BI (2014) Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des 28(3):265\u2013276","journal-title":"J Comput Aided Mol Des"},{"issue":"4","key":"9965_CR22","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1007\/s10822-014-9795-2","volume":"29","author":"E Gallicchio","year":"2015","unstructured":"Gallicchio E, Chen H, Chen H, Fitzgerald M, Gao Y, He P, Kalyanikar M, Kao C, Lu B, Niu Y, Pethe M, Zhu J, Levy RM (2015) BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J Comput Aided Mol Des 29(4):315\u2013325","journal-title":"J Comput Aided Mol Des"},{"issue":"13","key":"9965_CR23","doi-asserted-by":"publisher","first-page":"4770","DOI":"10.1021\/ja200633d","volume":"133","author":"H Gan","year":"2011","unstructured":"Gan H, Benjamin CJ, Gibb BC (2011) Nonmonotonic assembly of a deep-cavity cavitand. J Am Chem Soc 133(13):4770\u20134773","journal-title":"J Am Chem Soc"},{"issue":"4","key":"9965_CR24","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1007\/s10822-013-9690-2","volume":"28","author":"CLD Gibb","year":"2014","unstructured":"Gibb CLD, Gibb BC (2014) Binding of cyclic carboxylates to octa-acid deep-cavity cavitand. J Comput Aided Mol Des 28(4):319\u2013325","journal-title":"J Comput Aided Mol Des"},{"key":"9965_CR25","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1039\/b515187b","volume":"9","author":"ZR Laughrey","year":"2006","unstructured":"Laughrey ZR, Upton TG, Gibb BC (2006) A deuterated deep-cavity cavitand confirms the importance of C\u2013H\u22efX\u2013R hydrogen bonds in guest binding. Chem Commun 9:970\u2013972","journal-title":"Chem Commun"},{"issue":"24","key":"9965_CR26","doi-asserted-by":"publisher","first-page":"5849","DOI":"10.1021\/ja005931p","volume":"123","author":"CLD Gibb","year":"2001","unstructured":"Gibb CLD, Stevens ED, Gibb BC (2001) CH$$\\cdots$$XR (X=Cl, Br, and I) hydrogen bonds drive the complexation properties of a nanoscale molecular basket. J Am Chem Soc 123(24):5849\u20135850","journal-title":"J Am Chem Soc"},{"key":"9965_CR27","unstructured":"Gibb BC et al (2016) SAMPL5 experimental paper. J Comput Aided Mol Des"},{"issue":"4","key":"9965_CR28","first-page":"417","volume":"28","author":"H Hogues","year":"2014","unstructured":"Hogues H, Sulea T, Purisima EO (2014) Exhaustive docking and solvated interaction energy scoring: lessons learned from the sampl4 challenge. J Chem Inf Model 28(4):417\u2013427","journal-title":"J Chem Inf Model"},{"issue":"4","key":"9965_CR29","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1007\/s10822-014-9739-x","volume":"28","author":"P Mikulskis","year":"2014","unstructured":"Mikulskis P, Cioloboc D, Andreji\u0107 M, Khare S, Brorsson J, Genheden S, Mata RA, S\u00f6derhjelm P, Ryde U (2014) Free-energy perturbation and quantum mechanical study of sampl4 octa-acid host-guest binding energies. J Comput Aided Mol Des 28(4):375\u2013400","journal-title":"J Comput Aided Mol Des"},{"issue":"9","key":"9965_CR30","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","journal-title":"J Comput Chem"},{"key":"9965_CR31","unstructured":"Lee J, Tofoleanu F, K\u00f6nig G, Pickard FC IV, Huang J, Damjanovi\u0107 A, Baek M, Seok C, Brooks BR (2016) CBClip and guests. Same Issue"},{"issue":"4","key":"9965_CR32","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"K Vanommeslaeghe","year":"2010","unstructured":"Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell AD Jr (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31(4):671\u2013690","journal-title":"J Comput Chem"},{"key":"9965_CR33","doi-asserted-by":"publisher","unstructured":"Gutirrez IS, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL III, MacKerell AD Jr. (2016) Parametrization of halogen bonds in the CHARMM general force field: improved treatment of ligandprotein interactions. Bioorg Med Chem. doi: 10.1016\/j.bmc.2016.06.034","DOI":"10.1016\/j.bmc.2016.06.034"},{"issue":"2","key":"9965_CR34","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","journal-title":"J Chem Phys"},{"key":"9965_CR35","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/jcc.540040211","volume":"4","author":"BR Brooks","year":"1983","unstructured":"Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM\u2014a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187","journal-title":"J Comput Chem"},{"key":"9965_CR36","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks","year":"2009","unstructured":"Brooks BR, Brooks CL III, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodo\u0161\u010dek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545\u20131614","journal-title":"J Comput Chem"},{"key":"9965_CR37","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","volume":"31","author":"WG Hoover","year":"1985","unstructured":"Hoover WG (1985) Canonical dynamics\u2014equilibrium phase-space distributions. Phys Rev A 31:1695","journal-title":"Phys Rev A"},{"key":"9965_CR38","doi-asserted-by":"publisher","first-page":"4613","DOI":"10.1063\/1.470648","volume":"103","author":"SE Feller","year":"1995","unstructured":"Feller SE, Yhang YH, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613","journal-title":"J Chem Phys"},{"key":"9965_CR39","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1080\/00268977700102571","volume":"34","author":"WF van Gunsteren","year":"1977","unstructured":"van Gunsteren WF, Berendsen HJC (1977) Algorithms for macromolecular dynamics and costraint dynamics. Mol Phys 34:1311\u20131327","journal-title":"Mol Phys"},{"issue":"6","key":"9965_CR40","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1002\/jcc.20634","volume":"28","author":"R Huey","year":"2007","unstructured":"Huey R, Morris GM, Olson AJ, Goodsell DS (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28(6):1145\u20131152","journal-title":"J Comput Chem"},{"issue":"30","key":"9965_CR41","doi-asserted-by":"publisher","first-page":"2647","DOI":"10.1002\/jcc.23438","volume":"34","author":"W-H Shin","year":"2013","unstructured":"Shin W-H, Kim J-K, Kim D-S, Seok C (2013) GalaxyDock2: protein-ligand docking using beta-complex and global optimization. J Comput Chem 34(30):2647\u20132656","journal-title":"J Comput Chem"},{"key":"9965_CR42","unstructured":"Shin W-H, Lee GR, Seok C (2015) Evaluation of GalaxyDock based on the community structure activity resource 2013 and 2014 benchmark studies. J Chem Inf Model 56(6):988\u2013995"},{"issue":"9","key":"9965_CR43","doi-asserted-by":"publisher","first-page":"1222","DOI":"10.1002\/(SICI)1096-987X(19970715)18:9<1222::AID-JCC10>3.0.CO;2-7","volume":"18","author":"J Lee","year":"1997","unstructured":"Lee J, Scheraga HA, Rackovsky S (1997) New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J Comput Chem 18(9):1222\u20131232","journal-title":"J Comput Chem"},{"issue":"15","key":"9965_CR44","doi-asserted-by":"publisher","first-page":"3226","DOI":"10.1002\/jcc.21905","volume":"32","author":"W-H Shin","year":"2011","unstructured":"Shin W-H, Heo L, Lee J, Ko J, Seok C, Lee J (2011) Ligdockcsa: proteinligand docking using conformational space annealing. J Comput Chem 32(15):3226\u20133232","journal-title":"J Comput Chem"},{"key":"9965_CR45","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 72:1047\u20131069","journal-title":"Biophys J"},{"key":"9965_CR46","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 107:9535\u20139551","journal-title":"J Phys Chem B"},{"issue":"20","key":"9965_CR47","doi-asserted-by":"publisher","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 predictions. J Chem Phys 116(20):9058\u20139067","journal-title":"J Chem Phys"},{"key":"9965_CR48","doi-asserted-by":"publisher","first-page":"134105","DOI":"10.1063\/1.3372767","volume":"132","author":"SG Itoh","year":"2010","unstructured":"Itoh SG, Okumura H, Okamoto Y (2010) Replica-exchange in van der waals radius space: overcoming steric restrictions for biomolecules. J Chem Phys 132:134105","journal-title":"J Chem Phys"},{"key":"9965_CR49","doi-asserted-by":"publisher","first-page":"2493","DOI":"10.1002\/jcc.23402","volume":"34","author":"SG Itoh","year":"2013","unstructured":"Itoh SG, Okumura H (2013) Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-$$\\beta$$(29\u201342) peptides. J Comput Chem 34:2493\u20132497","journal-title":"J Comput Chem"},{"key":"9965_CR50","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1002\/jcc.21255","volume":"30","author":"G K\u00f6nig","year":"2009","unstructured":"K\u00f6nig G, Bruckner S, Boresch S (2009) Unorthodox uses of Bennett acceptance ratio method. J Comput Chem 30:1712\u20131718","journal-title":"J Comput Chem"},{"key":"9965_CR51","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1007\/s10822-011-9525-y","volume":"26","author":"G K\u00f6nig","year":"2012","unstructured":"K\u00f6nig G, Brooks BR (2012) Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. J Comput Aided Mol Des 26:543\u2013550","journal-title":"J Comput Aided Mol Des"},{"key":"9965_CR52","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/s10822-014-9708-4","volume":"28","author":"G K\u00f6nig","year":"2011","unstructured":"K\u00f6nig G, Pickard IV FC, Mei Y, Brooks BR (2011a) Predicting hydration free energies with a hybrid QM\/MM approach: an evaluation of implicit and explicit solvent models in sampl4. J Comput Aided Mol Des 28:245\u2013257","journal-title":"J Comput Aided Mol Des"},{"issue":"4","key":"9965_CR53","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1021\/ct401118k","volume":"10","author":"G K\u00f6nig","year":"2011","unstructured":"K\u00f6nig G, Hudson PS, Boresch S (2011b) Multiscale free energy simulations: an efficient method for connecting classical md simulations to QM or QM\/MM free energies using non-boltzmann bennett reweighting schemes. J Chem Theory Comput 10(4):1406\u20131419","journal-title":"J Chem Theory Comput"},{"issue":"4","key":"9965_CR54","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1016\/j.str.2009.02.010","volume":"17","author":"DL Mobley","year":"2009","unstructured":"Mobley DL, Dill KA (2009) Binding of small-molecule ligands to proteins: \u201cWhat you see\u201d is not always \u201cwhat you get\u201d. Structure 17(4):489\u2013498","journal-title":"Structure"},{"key":"9965_CR55","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1002\/jcc.21713","volume":"32","author":"S Bruckner","year":"2011","unstructured":"Bruckner S, Boresch S (2011) Efficiency of alchemical eree energy simulations I: practical comparison of the exponential formula, thermodynamic integration and Bennett\u2019s acceptance ratio method. J Comput Chem 32:1303\u20131319","journal-title":"J Comput Chem"},{"key":"9965_CR56","doi-asserted-by":"publisher","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":"9965_CR57","doi-asserted-by":"publisher","first-page":"9025","DOI":"10.1063\/1.466707","volume":"100","author":"M Zacharias","year":"1994","unstructured":"Zacharias M, Straatsma TP, Lennard-Jones JA (1994) Separation-shifted scaling, a new scaling method for lennard-jones interactions in thermodynamic integration. J Chem Phys 100:9025","journal-title":"J Chem Phys"},{"key":"9965_CR58","doi-asserted-by":"publisher","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 222:529\u2013539","journal-title":"Chem Phys Lett"},{"issue":"11","key":"9965_CR59","doi-asserted-by":"publisher","first-page":"2449","DOI":"10.1002\/jcc.21829","volume":"32","author":"S Boresch","year":"2011","unstructured":"Boresch S, Bruckner S (2011) Avoiding the van der Waals endpoint problem using serial atomic insertion. J Comput Chem 32(11):2449\u20132458","journal-title":"J Comput Chem"},{"issue":"6","key":"9965_CR60","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1007\/s00894-008-0386-9","volume":"15","author":"JS Murray","year":"2009","unstructured":"Murray JS, Lane P, Politzer P (2009) Expansion of the \u03c3-hole concept. J Mol Model 15(6):723\u2013729","journal-title":"J Mol Model"},{"issue":"1","key":"9965_CR61","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1002\/chem.200390008","volume":"9","author":"ZR Laughrey","year":"2003","unstructured":"Laughrey ZR, Gibb CLD, Senechal T, Gibb BC (2003) Guest binding and orientation within open nanoscale hosts. Chem Eur J 9(1):130\u2013139","journal-title":"Chem Eur J"},{"issue":"4","key":"9965_CR62","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1002\/chem.19970030421","volume":"3","author":"AMA van Wageningen","year":"1997","unstructured":"van Wageningen AMA, Timmerman P, van Duynhoven JPM, Verboom W, van Veggel FCJM, and Reinhoudt DN (1997) Calix[4]arene-based (hemi)carcerands and carceplexes: synthesis, functionalization, and molecular modeling study. Chem Eur J 3(4):639\u2013654","journal-title":"Chem Eur J"},{"issue":"50","key":"9965_CR63","doi-asserted-by":"publisher","first-page":"8905","DOI":"10.1016\/S0040-4039(99)01928-0","volume":"40","author":"K Paek","year":"1999","unstructured":"Paek K, Ihm H, Yun S, Lee HC (1999) Carceroisomerism and twistomerism in $${\\text{ C }}_{4v}$$ tetraoxatetrathiahemicarceplexes. Tetrahedron Lett. 40(50):8905\u20138909","journal-title":"Tetrahedron Lett."},{"issue":"17","key":"9965_CR64","doi-asserted-by":"publisher","first-page":"6290","DOI":"10.1073\/pnas.0711686105","volume":"105","author":"D Jiao","year":"2008","unstructured":"Jiao D, Golubkov PA, Darden TA, Ren P (2008) Calculation of proteinligand binding free energy by using a polarizable potential. Proc Natl Acad Sci USA 105(17):6290\u20136295","journal-title":"Proc Natl Acad Sci USA"},{"key":"9965_CR65","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1146\/annurev.biophys.36.040306.132550","volume":"36","author":"MK Gilson","year":"2007","unstructured":"Gilson MK, Zhou H-X (2007) Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 36:21\u201342","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"9965_CR66","unstructured":"Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, Jr., Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J. and Fox DJ (2010) Gaussian 09, Revision B.01, Gaussian, Inc., Wallingford"},{"key":"9965_CR67","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/s00214-007-0310-x","volume":"120","author":"Y Zhao","year":"2007","unstructured":"Zhao Y, Truhlar DG (2007) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other function. Theor Chem Acc 120:215\u2013241","journal-title":"Theor Chem Acc"},{"key":"9965_CR68","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1021\/ar700111a","volume":"41","author":"Y Zhao","year":"2008","unstructured":"Zhao Y, Truhlar DG (2008) Density functionals with broad applicability in chemistry. Acc Chem Res 41:157\u2013167","journal-title":"Acc Chem Res"},{"issue":"18","key":"9965_CR69","doi-asserted-by":"publisher","first-page":"6378","DOI":"10.1021\/jp810292n","volume":"113","author":"AV Marenich","year":"2009","unstructured":"Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113(18):6378\u20136396","journal-title":"J Phys Chem B"},{"issue":"1","key":"9965_CR70","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1080\/00268977400100171","volume":"27","author":"PC Hariharan","year":"1974","unstructured":"Hariharan PC, Pople JA (1974) Accuracy of $$\\text{ AH }_{n}$$ equilibrium geometries by single determinant molecular orbital theory. Mol Phys 27(1):209\u2013214","journal-title":"Mol Phys"},{"issue":"20","key":"9965_CR71","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1002\/qua.24699","volume":"114","author":"R Casasnovas","year":"2014","unstructured":"Casasnovas R, Ortega-Castro J, Frau J, Donoso J, Muoz F (2014) Theoretical pKa calculations with continuum model solvents, alternative protocols to thermodynamic cycles. Int J Quantum Chem 114(20):1350\u20131363","journal-title":"Int J Quantum Chem"},{"issue":"30","key":"9965_CR72","doi-asserted-by":"publisher","first-page":"7314","DOI":"10.1021\/ja010534f","volume":"123","author":"MD Liptak","year":"2001","unstructured":"Liptak MD, Shields GC (2001) Accurate pK(a) calculations for carboxylic acids using complete basis set and Gaussian-n models combined with CPCM continuum solvation methods. J Am Chem Soc 123(30):7314\u20137319","journal-title":"J Am Chem Soc"},{"key":"9965_CR73","volume-title":"Ionization constants of inorganic acids and bases in aqueous solution","author":"DD Perrin","year":"1982","unstructured":"Perrin DD (1982) Ionization constants of inorganic acids and bases in aqueous solution, 2nd edn. Pergamon, Oxford","edition":"2"},{"key":"9965_CR74","unstructured":"Majstorovic V (2011) Changes in high-molecular weight compounds during beech litter decomposition. Masters thesis"},{"key":"9965_CR75","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1039\/C4SC02090A","volume":"6","author":"W Cullen","year":"2015","unstructured":"Cullen W, Turega S, Hunter CA, Ward MD (2015) pH-dependent binding of guests in the cavity of a polyhedral coordination cage: reversible uptake and release of drug molecules. Chem Sci 6:625\u2013631","journal-title":"Chem Sci"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9965-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-016-9965-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9965-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,19]],"date-time":"2024-06-19T17:59:11Z","timestamp":1718819951000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-016-9965-5"}},"subtitle":["Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge"],"short-title":[],"issued":{"date-parts":[[2016,9,30]]},"references-count":75,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,1]]}},"alternative-id":["9965"],"URL":"https:\/\/doi.org\/10.1007\/s10822-016-9965-5","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2016,9,30]]},"assertion":[{"value":"21 June 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}