{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T12:46:42Z","timestamp":1761310002110,"version":"3.41.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[1999,3,1]],"date-time":"1999-03-01T00:00:00Z","timestamp":920246400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[1999,3,1]],"date-time":"1999-03-01T00:00:00Z","timestamp":920246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[1999,3]]},"DOI":"10.1023\/a:1008044721715","type":"journal-article","created":{"date-parts":[[2002,12,22]],"date-time":"2002-12-22T12:45:23Z","timestamp":1040561123000},"page":"109-121","source":"Crossref","is-referenced-by-count":23,"title":["Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations"],"prefix":"10.1007","volume":"13","author":[{"given":"Margaret A.","family":"McCarrick","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter A.","family":"Kollman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"188481_CR1","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1126\/science.2405486","volume":"247","author":"T.J. McQuade","year":"1990","unstructured":"McQuade, T.J., Thomasselli, A.G, Liu, L., Karacostas, V., Moss, B., Sawyer, T.K., Heinrikson, R.L. and Tarpley, W.G., Science, 247 (1990) 454.","journal-title":"Science"},{"key":"188481_CR2","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/337615a0","volume":"337","author":"M.A. Navia","year":"1989","unstructured":"Navia, M.A., Fitzgerald, P.M.D., Mc Keever, B.M., Leu, C.-T., Heimbach, J.C., Herber, W.K., Sigal, I.S., Darke, P.L. and Springer, J.P., Nature, 337 (1989) 615.","journal-title":"Nature"},{"key":"188481_CR3","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1126\/science.2548279","volume":"245","author":"A. Wlodawer","year":"1989","unstructured":"Wlodawer, A., Miller, M., Jaskolski, M., Sathyanarayana, B.K., Baldwin, E., Weber, I.T., Selk, L.M., Clawson, L., Schneider, J. and Kent, S.B.H., Science, 245 (1989) 616.","journal-title":"Science"},{"key":"188481_CR4","doi-asserted-by":"crossref","first-page":"8805","DOI":"10.1073\/pnas.87.22.8805","volume":"87","author":"A.L. Swain","year":"1990","unstructured":"Swain, A.L., Miller, M.M., Green, J., Rich, D.H., Schneider, J., Kent, S.B.H. and Wlodawer, A., Proc. Natl. Acad. Sci. USA, 87 (1990) 8805.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"188481_CR5","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1126\/science.2686029","volume":"246","author":"M. Miller","year":"1989","unstructured":"Miller, M., Schneider, J., Sathyanarayana, B.K., Toth, M.V., Marshall, G.R., Clawson, L., Selk, L., Kent, S.B.H. and Wlodawer, A., Science, 246 (1989) 1149.","journal-title":"Science"},{"key":"188481_CR6","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1021\/bi00220a023","volume":"30","author":"M. Jaskolski","year":"1991","unstructured":"Jaskolski, M., Tomasselli, A.G., Sawyer, T.K., Staples, D.G., Heinrikson, R.L., Schneider, J., Kent, S.B.H. and Wlodawer, A., Biochemistry, 30 (1991) 1600.","journal-title":"Biochemistry"},{"key":"188481_CR7","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/0076-6879(94)41074-7","volume":"241","author":"M.A. McCarrick","year":"1994","unstructured":"For a review, see McCarrick, M.A. and Kollman, P.A., Methods Enzymol., 241 (1994) 370.","journal-title":"Methods Enzymol."},{"key":"188481_CR8","doi-asserted-by":"crossref","first-page":"2654","DOI":"10.1021\/jm00112a048","volume":"34","author":"D.M. Ferguson","year":"1991","unstructured":"Ferguson, D.M., Radmer, R.J. and Kollman, P.A., J. Med. Chem., 34 (1991) 2654.","journal-title":"J. Med. Chem."},{"key":"188481_CR9","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/protein\/5.1.29","volume":"5","author":"A. Tropsha","year":"1992","unstructured":"Tropsha, A. and Hermans, J., Protein Eng., 5 (1992) 29.","journal-title":"Protein Eng."},{"key":"188481_CR10","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1021\/jm00107a049","volume":"34","author":"D.H. Rich","year":"1991","unstructured":"Rich, D.H., Sun, C.Q., Vara Prasad, J.V.N., Pathiasseril, A., Toth, M.V., Marshall, G.R., Clare, M., Mueller, R.A. and Houseman, K., J. Med. Chem., 34 (1991) 1222.","journal-title":"J. Med. Chem."},{"key":"188481_CR11","doi-asserted-by":"crossref","first-page":"10287","DOI":"10.1073\/pnas.88.22.10287","volume":"88","author":"M.R. Reddy","year":"1991","unstructured":"Reddy, M.R., Viswanadhan, V.N. and Weinstein, J.N., Proc. Natl. Acad. Sci. USA, 88 (1991) 10287.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"188481_CR12","doi-asserted-by":"crossref","first-page":"4447","DOI":"10.1021\/ja00038a001","volume":"114","author":"B.G. Rao","year":"1992","unstructured":"Rao, B.G., Tilton, R.F. and Singh, U.C., J. Am. Chem. Soc., 114 (1992) 4447.","journal-title":"J. Am. Chem. Soc."},{"key":"188481_CR13","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1021\/jm00001a009","volume":"38","author":"X Chen","year":"1995","unstructured":"Chen, X and Tropsha, A., J. Med. Chem., 38 (1995) 42.","journal-title":"J. Med. Chem."},{"key":"188481_CR14","doi-asserted-by":"crossref","first-page":"6644","DOI":"10.1073\/pnas.87.17.6644","volume":"87","author":"R.L. Desjarlais","year":"1990","unstructured":"Desjarlais, R.L., Seibel, G.L., Kuntz, I.D., Furth, P.S., Alvarez, J.C., Ortiz de Montellano, P.R., DeCamp, D.L., Babe, L.M. and Craik, C.S., Proc. Natl. Acad. Sci. USA, 87 (1990) 6644.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"188481_CR15","doi-asserted-by":"crossref","first-page":"15343","DOI":"10.1016\/S0021-9258(18)82261-X","volume":"268","author":"E. Rutenber","year":"1993","unstructured":"Rutenber, E., Fauman, E.B., Keenan, R.J., Fong, S., Furth, P.S., Ortiz de Montellano, P.R., Meng, E., Kuntz, I.D., De-Camp, D.L., Salto, R., Rose, J.R., Craik, C.S. and Stroud, R.M., J. Biol. Chem., 268 (1993) 15343.","journal-title":"J. Biol. Chem."},{"key":"188481_CR16","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/0263-7855(88)80054-7","volume":"6","author":"T.E. Ferrin","year":"1988","unstructured":"Ferrin, T.E., Huang, C.C., Jarvis, L.E. and Langridge, R., J. Mol. Graphics, 6 (1988) 13.","journal-title":"J. Mol. Graphics"},{"key":"188481_CR17","first-page":"1","volume":"91","author":"D.A. Pearlman","year":"1995","unstructured":"Pearlman, D.A., Caldwell, J.W., Case, D.A., Ross, W.S., Cheatham III, T.E., DeBolt, S., Ferguson, D., Seibel, G. and Kollman, P.A., Comput. Phys. Lett., 91 (1995) 1.","journal-title":"Comput. Phys. Lett."},{"key":"188481_CR18","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1021\/ja00315a051","volume":"106","author":"S.J. Weiner","year":"1984","unstructured":"Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S. and Weiner, P., J. Am. Chem. Soc., 106 (1984) 765.","journal-title":"Am. Chem. Soc."},{"key":"188481_CR19","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1002\/jcc.540070216","volume":"7","author":"S.J. Weiner","year":"1986","unstructured":"Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A., J. Comput. Chem., 7 (1986) 230.","journal-title":"J. Comput. Chem."},{"key":"188481_CR20","doi-asserted-by":"crossref","first-page":"8551","DOI":"10.1021\/ja00205a001","volume":"111","author":"N.L. Allinger","year":"1989","unstructured":"Allinger, N.L., Yuh, Y.H. and Li, J.H., J. Am. Chem. Soc., 111 (1989) 8551.","journal-title":"J. Am. Chem. Soc."},{"key":"188481_CR21","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1002\/jcc.540130806","volume":"13","author":"C. Gough","year":"1992","unstructured":"Gough, C., DeBolt, S. and Kollman, P.A., J. Comput. Chem., 13 (1992) 963.","journal-title":"J. Comput. Chem."},{"key":"188481_CR22","doi-asserted-by":"crossref","first-page":"10269","DOI":"10.1021\/j100142a004","volume":"97","author":"C. Bayly","year":"1993","unstructured":"Bayly, C., Cieplak, P., Cornell, W.D. and Kollman, P.A., J. Phys. Chem., 97 (1993) 10269.","journal-title":"J. Phys. Chem."},{"key":"188481_CR23","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"W. Jorgensen","year":"1983","unstructured":"Jorgensen, W., Chandrasekhar, J., Madura, J., Impey, R. and Klein, M., J. Chem. Phys., 79 (1983) 926.","journal-title":"J. Chem. Phys."},{"key":"188481_CR24","unstructured":"Several such reviews are"},{"key":"188481_CR25","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1146\/annurev.pc.43.100192.002203","volume":"43","author":"T.P. Straatsma","year":"1992","unstructured":"Straatsma, T.P. and McCammon, J.A., Annu Rev. Phys. Chem., 43, (1992) 407.","journal-title":"Annu Rev. Phys. Chem."},{"key":"188481_CR26","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1017\/S0269727000013087","volume":"99","author":"W.G. Richards","year":"1992","unstructured":"Richards, W.G., Proc. R. Soc. Edinburgh Sec. B, Biol. Sci., 99 (1992) 105.","journal-title":"Proc. R. Soc. Edinburgh Sec. B, Biol. Sci."},{"key":"188481_CR27","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1021\/cr00023a004","volume":"93","author":"P.A. Kollman","year":"1993","unstructured":"Kollman, P.A., Chem. Rev., 93 (1993) 2395.","journal-title":"Chem. Rev."},{"key":"188481_CR28","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1146\/annurev.bb.18.060189.002243","volume":"18","author":"D.L. Beveridge","year":"1989","unstructured":"Beveridge, D.L. and DiCapua, F.M., Annu. Rev. Biophys. Biophys. Chem., 18 (1989) 431.","journal-title":"Annu. Rev. Biophys. Biophys. Chem."},{"key":"188481_CR29","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1080\/07391102.1993.10508728","volume":"11","author":"S. Singh","year":"1993","unstructured":"Singh, S., Pearlman, D.A. and Kollman, P.A., J. Biomol. Struct. Dyn., 11 (1993) 303.","journal-title":"J. Biomol. Struct. Dyn."},{"key":"188481_CR30","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1021\/ja00119a045","volume":"117","author":"T.E. Cheatham III","year":"1995","unstructured":"Cheatham III, T.E., Miller, J.L., Fox, T., Darden, T.A. and Kollman, P.A., J. Am. Chem. Soc., 117 (1995) 4193.","journal-title":"J. Am. Chem. Soc."},{"key":"188481_CR31","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1093\/protein\/9.3.273","volume":"9","author":"Y. Sun","year":"1995","unstructured":"Sun, Y., Veenstra, D.L. and Kollman, P.A., Protein Eng., 9 (1995) 273.","journal-title":"Protein Eng."},{"key":"188481_CR32","doi-asserted-by":"crossref","first-page":"2605","DOI":"10.1021\/jp952516o","volume":"100","author":"K.N. Allen","year":"1996","unstructured":"Allen, K.N., Bellamacina, C.R., Ding, X.C., Jeffrey, C.J., Mattos, C., Petsko, G.A. and Ringe, D., J. Phys. Chem., 100 (1996) 2605.","journal-title":"J. Phys. Chem."},{"key":"188481_CR33","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1021\/jm9509197","volume":"39","author":"M. Driscoll","year":"1996","unstructured":"Driscoll, M., Seddiqui, H., Ford, J., Kelley, J., Roth, H., Mitsuya, M., Tanaka and Marquez, V., J. Med. Chem., 39 (1996) 1619.","journal-title":"J. Med. Chem."}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1023\/A:1008044721715.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1023\/A:1008044721715\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1023\/A:1008044721715.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T11:34:58Z","timestamp":1749123298000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1023\/A:1008044721715"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[1999,3]]},"references-count":33,"journal-issue":{"issue":"2","published-print":{"date-parts":[[1999,3]]}},"alternative-id":["188481"],"URL":"https:\/\/doi.org\/10.1023\/a:1008044721715","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[1999,3]]}}}