{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T20:46:17Z","timestamp":1762375577881},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2012,2,16]],"date-time":"2012-02-16T00:00:00Z","timestamp":1329350400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2012,5]]},"DOI":"10.1007\/s10822-012-9542-5","type":"journal-article","created":{"date-parts":[[2012,2,15]],"date-time":"2012-02-15T10:45:52Z","timestamp":1329302752000},"page":"569-576","source":"Crossref","is-referenced-by-count":26,"title":["Thermodynamic integration to predict host-guest binding affinities"],"prefix":"10.1007","volume":"26","author":[{"given":"Morgan","family":"Lawrenz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeff","family":"Wereszczynski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan Manuel","family":"Ortiz-S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara E.","family":"Nichols","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. Andrew","family":"McCammon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,2,16]]},"reference":[{"key":"9542_CR1","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1146\/annurev.bb.18.060189.002243","volume":"L18","author":"D Beveridge","year":"1989","unstructured":"Beveridge D, DiCapua F (1989) Free energy via molecular simulation: application to chemical and biomolecular systems. Annu Rev Biophys Chem L18:431\u2013492","journal-title":"Annu Rev Biophys Chem"},{"key":"9542_CR2","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1021\/cr00023a004","volume":"L93","author":"P Kollman","year":"1993","unstructured":"Kollman P (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev L93:2395\u20132417","journal-title":"Chem Rev"},{"key":"9542_CR3","volume-title":"Computation of free energy in practice: choice of approximations and accuracy limiting factors, vol 2","author":"WF Gunsteren van","year":"1993","unstructured":"van Gunsteren WF, Beutler TC, Fraternali F, King PM, Mark AE, Smith PE (1993) Computation of free energy in practice: choice of approximations and accuracy limiting factors, vol 2. ESCOM Science Publishers, Leiden"},{"key":"9542_CR4","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1016\/S0006-3495(97)78756-3","volume":"L72","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 L72:1047\u20131069","journal-title":"Biophys J"},{"key":"9542_CR5","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1126\/science.1096361","volume":"L303","author":"W Jorgensen","year":"2004","unstructured":"Jorgensen W (2004) The many roles of computation in drug discovery. Science L303:1813\u20131818","journal-title":"Science"},{"key":"9542_CR6","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1146\/annurev.biophys.36.040306.132550","volume":"L36","author":"MK Gilson","year":"2007","unstructured":"Gilson MK, Zhou H-X (2007) Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct L36:21\u201342","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"9542_CR7","doi-asserted-by":"crossref","first-page":"10235","DOI":"10.1021\/jp102971x","volume":"L114","author":"A Pohorille","year":"2010","unstructured":"Pohorille A, Jarzynski C, Chipot C (2010) Good practices in free-energy calculations. J Phys Chem B L114:10235\u201310253","journal-title":"J Phys Chem B"},{"key":"9542_CR8","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1002\/jcc.21450","volume":"L31","author":"CD Christ","year":"2010","unstructured":"Christ CD, Mark AE, Gunsteren WFV (2010) Basic ingredients of free energy calculations: a review. J Comput Chem L31:1569\u20131582","journal-title":"J Comput Chem"},{"key":"9542_CR9","doi-asserted-by":"crossref","first-page":"4012","DOI":"10.1021\/ja808175m","volume":"L131","author":"S Moghaddam","year":"2009","unstructured":"Moghaddam S, Inoue Y, Gilson MK (2009) Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc L131:4012\u20134021","journal-title":"J Am Chem Soc"},{"key":"9542_CR10","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1063\/1.1749657","volume":"L3","author":"JG Kirkwood","year":"1935","unstructured":"Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys L3:300\u2013313","journal-title":"J Chem Phys"},{"key":"9542_CR11","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/0097-8485(84)85020-2","volume":"L8","author":"B Tembe","year":"1984","unstructured":"Tembe B, McCammon J (1984) Ligand receptor interactions. J Comput Chem L8:281\u2013283","journal-title":"J Comput Chem"},{"key":"9542_CR12","doi-asserted-by":"crossref","first-page":"084108","DOI":"10.1063\/1.1999637","volume":"L123","author":"H Fujitani","year":"2005","unstructured":"Fujitani H, Tanida Y, Ito M, Jayachandran G, Snow CD, Shirts MR, Sorin EJ, Pande VS (2005) Direct calculation of the binding free energies of FKBP ligands. J Chem Phys L123:084108","journal-title":"J Chem Phys"},{"key":"9542_CR13","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1021\/ct600322d","volume":"L3","author":"B Zagrovic","year":"2007","unstructured":"Zagrovic B, van Gunsteren W (2007) Computational analysis of the mechanism and thermodynamics of inhibition of phosphodiesterase 5A by synthetic ligands. J Chem Theory Comput L3:301\u2013311","journal-title":"J Chem Theory Comput"},{"key":"9542_CR14","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1021\/ct800559d","volume":"L5","author":"M Lawrenz","year":"2009","unstructured":"Lawrenz M, Baron R, McCammon J (2009) Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir. J Chem Theory Comput L5:1106\u20131116","journal-title":"J Chem Theory Comput"},{"key":"9542_CR15","doi-asserted-by":"crossref","first-page":"4786","DOI":"10.1021\/jo100760g","volume":"L75","author":"D Ma","year":"2010","unstructured":"Ma D, Zavalij PY, Isaacs L (2010) Acyclic cucurbit[n]uril congeners are high affinity hosts. J Org Chem L75:4786\u20134795","journal-title":"J Org Chem"},{"key":"9542_CR16","doi-asserted-by":"crossref","first-page":"7683","DOI":"10.1021\/ja0377908","volume":"L126","author":"D Hamelberg","year":"2004","unstructured":"Hamelberg D, McCammon JA (2004) Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc L126:7683\u20137689","journal-title":"J Am Chem Soc"},{"key":"9542_CR17","unstructured":"LigPrep version 2.3; Schrodinger LLC: New York, NY, (2009)"},{"key":"9542_CR18","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","volume":"L47","author":"RA Friesner","year":"2004","unstructured":"Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem L47:1739\u20131749","journal-title":"J Med Chem"},{"key":"9542_CR19","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1021\/jm030644s","volume":"L47","author":"TA Halgren","year":"2004","unstructured":"Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem L47:1750\u20131759","journal-title":"J Med Chem"},{"key":"9542_CR20","doi-asserted-by":"crossref","first-page":"6177","DOI":"10.1021\/jm051256o","volume":"L49","author":"RA Friesner","year":"2006","unstructured":"Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem L49:6177\u20136196","journal-title":"J Med Chem"},{"key":"9542_CR21","volume-title":"AMBER 11","author":"DA Case","year":"2010","unstructured":"Case DA et\u00a0al (2010) AMBER 11. University of California, San Francisco"},{"key":"9542_CR22","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"L25","author":"J Wang","year":"2004","unstructured":"Wang J, Wolf RM, Caldwell JW, Case PAKDA (2004) Development and testing of a general amber force field. J Comput Chem L25:1157\u20131174","journal-title":"J Comput Chem"},{"key":"9542_CR23","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1021\/ja00124a002","volume":"L117","author":"WD Cornell","year":"1995","unstructured":"Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc L117:5179\u20135197","journal-title":"J Am Chem Soc"},{"key":"9542_CR24","volume-title":"Gaussian 03, Revision C02:2003","author":"M Frisch","year":"2004","unstructured":"Frisch M et\u00a0al (2004) Gaussian 03, Revision C02:2003. Gaussian Inc., Wallingford"},{"key":"9542_CR25","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"L79","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 L79:926\u2013935","journal-title":"J Chem Phys"},{"key":"9542_CR26","doi-asserted-by":"crossref","first-page":"8021","DOI":"10.1021\/j100384a009","volume":"L94","author":"J \u00c5qvist","year":"1990","unstructured":"\u00c5qvist J (1990) Ion-water interaction potentials derived from free energy perturbation simulations. J Phys Chem L94:8021\u20138024","journal-title":"J Phys Chem"},{"key":"9542_CR27","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"L26","author":"JC Phillips","year":"2005","unstructured":"Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kal\u00e9 L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem L26:1781\u20131802","journal-title":"J Comput Chem"},{"key":"9542_CR28","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/0021-9991(83)90014-1","volume":"L52","author":"H Andersen","year":"1983","unstructured":"Andersen H (1983) Rattle: a \"velocity\" version of the shake algorithm for molecular dynamics calculations. J Comput Phys L52:24\u201334","journal-title":"J Comput Phys"},{"key":"9542_CR29","unstructured":"Shuichi M, Peter A (1992) SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem L13:952\u2013962, 148324"},{"key":"9542_CR30","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","volume":"L98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N [center-dot] log(N) method for Ewald sums in large systems. J Chem Phys L98:10089\u201310092","journal-title":"J Chem Phys"},{"key":"9542_CR31","doi-asserted-by":"crossref","first-page":"4613","DOI":"10.1063\/1.470648","volume":"L103","author":"S Feller","year":"1995","unstructured":"Feller S, Zhang Y, Pastor R, Brooks B (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys L103:4613\u20134621","journal-title":"J Chem Phys"},{"key":"9542_CR32","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1063\/1.1749657","volume":"L3","author":"J. Kirkwood","year":"1935","unstructured":"Kirkwood J (1935) Statistical mechanics of fluid mixtures. J Chem Phys L3:300\u2013313","journal-title":"J Chem Phys"},{"key":"9542_CR33","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1021\/ct200230v","volume":"L7","author":"M Lawrenz","year":"2011","unstructured":"Lawrenz M, Baron R, Wang Y, McCammon JA (2011) Effects of biomolecular flexibility on alchemical calculations of absolute binding free energies. J Chem Theory Comput L7:2224\u20132232","journal-title":"J Chem Theory Comput"},{"key":"9542_CR34","doi-asserted-by":"crossref","first-page":"9025","DOI":"10.1063\/1.466707","volume":"L100","author":"M Zacharias","year":"1994","unstructured":"Zacharias M, Straatsma TP, McCammon JA (1994) Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J Chem Phys L100:9025\u20139031","journal-title":"J Chem Phys"},{"key":"9542_CR35","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1021\/ct0502864","volume":"L3","author":"J Chodera","year":"2007","unstructured":"Chodera J, Swope W, Pitera J, Seok C, Dill K (2007) Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J Chem Theory Comput L3:26\u201341. doi: 10.1021\/ct0502864","journal-title":"J Chem Theory Comput"},{"key":"9542_CR36","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1214\/aos\/1176350057","volume":"L14","author":"E Carlstein","year":"1986","unstructured":"Carlstein E (1986) The use of subseries values for estimating the variance of a general statistic from a stationary sequence. Ann Stat L14:1171\u20131179","journal-title":"Ann Stat"},{"key":"9542_CR37","doi-asserted-by":"crossref","first-page":"9535","DOI":"10.1021\/jp0217839","volume":"L107","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 L107:9535\u20139551","journal-title":"J Phys Chem B"},{"key":"9542_CR38","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1021\/ct100255z","volume":"L6","author":"IJ General","year":"2010","unstructured":"General IJ (2010) A note on the standard state\u2019s binding free energy. J Chem Theory Comput L6:2520\u20132524","journal-title":"J Chem Theory Comput"},{"key":"9542_CR39","doi-asserted-by":"crossref","unstructured":"Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graphics L14:33\u201338, 27\u201328","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"9542_CR40","doi-asserted-by":"crossref","first-page":"1856","DOI":"10.1063\/1.477873","volume":"L110","author":"PH H\u00fcnenberger","year":"1999","unstructured":"H\u00fcnenberger PH, McCammon JA (1999) Ewald artifacts in computer simulations of ionic solvation and ion\u2013ion interaction: a continuum electrostatics study. J Chem Phys L110:1856","journal-title":"J Chem Phys"},{"key":"9542_CR41","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1021\/jp951011v","volume":"L100","author":"G Hummer","year":"1996","unstructured":"Hummer G, Pratt LR, Garc\u00eda AE (1996) Free energy of ionic hydration. J Phys Chem L100:1206\u20131215","journal-title":"J Phys Chem"},{"key":"9542_CR42","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","volume":"L4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput L4:435\u2013447","journal-title":"J Chem Theory Comput"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-012-9542-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-012-9542-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-012-9542-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,19]],"date-time":"2024-04-19T19:30:01Z","timestamp":1713555001000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-012-9542-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2,16]]},"references-count":42,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2012,5]]}},"alternative-id":["9542"],"URL":"https:\/\/doi.org\/10.1007\/s10822-012-9542-5","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,2,16]]}}}