{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T09:18:50Z","timestamp":1774084730170,"version":"3.50.1"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2006,9,1]],"date-time":"2006-09-01T00:00:00Z","timestamp":1157068800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2006,9,1]],"date-time":"2006-09-01T00:00:00Z","timestamp":1157068800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2006,9]]},"DOI":"10.1007\/s10822-006-9082-y","type":"journal-article","created":{"date-parts":[[2006,10,18]],"date-time":"2006-10-18T13:59:06Z","timestamp":1161179946000},"page":"567-587","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":167,"title":["GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D"],"prefix":"10.1007","volume":"20","author":[{"given":"Nicola J.","family":"Richmond","sequence":"first","affiliation":[]},{"given":"Charlene A.","family":"Abrams","sequence":"additional","affiliation":[]},{"given":"Philippa R. N.","family":"Wolohan","sequence":"additional","affiliation":[]},{"given":"Edmond","family":"Abrahamian","sequence":"additional","affiliation":[]},{"given":"Peter","family":"Willett","sequence":"additional","affiliation":[]},{"given":"Robert D.","family":"Clark","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,10,19]]},"reference":[{"key":"9082_CR1","volume-title":"3D QSAR in drug design","year":"1998","unstructured":"Kubinyi H, Folkers G, Martin YC (eds) (1998) 3D QSAR in drug design. Kluwer\/ESCOM, Leiden"},{"key":"9082_CR2","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1023\/A:1008026308790","volume":"11","author":"AM Ferguson","year":"1997","unstructured":"Ferguson AM, Heritage T, Jonathon P, Pack SE, Phillips L, Rogan J, Snaith PJ (1997) J Comput Aided Mol Des 11:143","journal-title":"J Comput Aided Mol Des"},{"key":"9082_CR3","doi-asserted-by":"publisher","first-page":"3233","DOI":"10.1021\/jm000941m","volume":"43","author":"M Pastor","year":"2000","unstructured":"Pastor M, Cruciani G, McLay I, Pickett S, Clementi S (2000) J Med Chem 43:3233","journal-title":"J Med Chem"},{"key":"9082_CR4","doi-asserted-by":"publisher","first-page":"5959","DOI":"10.1021\/ja00226a005","volume":"110","author":"RD Cramer III","year":"1988","unstructured":"Cramer RD III, Patterson DE, Bunce JD (1988) J Am Chem Soc 110:5959","journal-title":"J Am Chem Soc"},{"key":"9082_CR5","doi-asserted-by":"publisher","first-page":"4130","DOI":"10.1021\/jm00050a010","volume":"37","author":"G Klebe","year":"1994","unstructured":"Klebe G, Abraham U, Mietzner T (1994) J Med Chem 37:4130","journal-title":"J Med Chem"},{"key":"9082_CR6","unstructured":"Clark RD, Abrahamian E, Strizhev A, Wolohan PRN, Abrams C (2005) 230th ACS National Meeting, Washington, COMP 137"},{"key":"9082_CR7","unstructured":"Clark RD, Abrahamian E, Abrams C, Brandt P, Gustavsson A-L, Homan E, Metwally E, Richmond NJ, Strizhev A, Wirstam M, Wolohan P (manuscript in preparation)"},{"key":"9082_CR8","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1023\/A:1008194019144","volume":"14","author":"C Lemmen","year":"2000","unstructured":"Lemmen C, Lengauer T (2000) J Comput Aided Mol Des 14:215","journal-title":"J Comput Aided Mol Des"},{"key":"9082_CR9","doi-asserted-by":"crossref","unstructured":"Vladutz G, Gould SR (1988) In: Warr WA (ed) Chemical structures. The international language of chemistry. Springer, Berlin Heidelberg New York, pp 371\u2013384","DOI":"10.1007\/978-3-642-73975-0_39"},{"key":"9082_CR10","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1021\/ci00017a006","volume":"34","author":"RD Brown","year":"1994","unstructured":"Brown RD, Downs GM, Jones G, Willett P (1994) J Chem Inf Comput Sci 34:47","journal-title":"J Chem Inf Comput Sci"},{"key":"9082_CR11","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1021\/ci0103875","volume":"43","author":"N Brown","year":"2003","unstructured":"Brown N, Willett P, Wilton DJ, Lewis RA (2003) J Chem Inf Comput Sci 43:288","journal-title":"J Chem Inf Comput Sci"},{"key":"9082_CR12","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1021\/ci980114i","volume":"40","author":"VA Palyulin","year":"2000","unstructured":"Palyulin VA, Radchenko EV, Zefirov NS (2000) J Chem Inf Comput Sci 40:659","journal-title":"J Chem Inf Comput Sci"},{"key":"9082_CR13","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1023\/A:1021271615909","volume":"16","author":"JW Raymond","year":"2002","unstructured":"Raymond JW, Willett P (2002) J Comput Aided Mol Des 16:521","journal-title":"J Comput Aided Mol Des"},{"key":"9082_CR14","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.jmgm.2004.04.004","volume":"23","author":"NJ Richmond","year":"2004","unstructured":"Richmond NJ, Willett P, Clark RD (2004) J Mol Graph Model 23:199","journal-title":"J Mol Graph Model"},{"key":"9082_CR15","unstructured":"GALAHAD\u2122 is distributed by Tripos, Inc., 1699 S. Hanley Rd., St. Louis MO 63144 USA, http:\/\/www.tripos.com"},{"key":"9082_CR16","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1023\/A:1021954728347","volume":"16","author":"Y Patel","year":"2002","unstructured":"Patel Y, Gillet V, Bravi G, Leach AR (2002) J Comput Aided Mol Des 16:653","journal-title":"J Comput Aided Mol Des"},{"key":"9082_CR17","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1109\/34.993558","volume":"24","author":"S Belongie","year":"2002","unstructured":"Belongie S, Malik J, Puzicha J (2002) IEEE Trans Pattern Anal Mach Intell 24:509","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"9082_CR18","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1021\/ci025595r","volume":"43","author":"E Abrahamian","year":"2003","unstructured":"Abrahamian E, Fox PC, N\u00e6rum L, Christensen IT, Th\u00f8gersen H, Clark RD (2003) J Chem Inf Comput Sci 43:458","journal-title":"J Chem Inf Comput Sci"},{"key":"9082_CR19","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/comjnl\/26.4.354","volume":"26","author":"F Murtagh","year":"1983","unstructured":"Murtagh F (1983) Comput J 26:354","journal-title":"Comput J"},{"key":"9082_CR20","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1021\/ci00010a010","volume":"32","author":"JM Barnard","year":"1992","unstructured":"Barnard JM, Downs GM (1992) J Chem Inf Comput Sci 32:644","journal-title":"J Chem Inf Comput Sci"},{"key":"9082_CR21","unstructured":"Individual molecules have conformations but the accompanying position in space\u2014the configuration\u2014is only meaningful in relation to another molecule, e.g., in complex with a protein or in a hypermolecular alignment"},{"key":"9082_CR22","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1007\/BF00124324","volume":"9","author":"G Jones","year":"1995","unstructured":"Jones G, Willett P, Glen RC (1995) J Comput Aided Mol Des 9:532","journal-title":"J Comput Aided Mol Des"},{"key":"9082_CR23","unstructured":"GASP\u2122 is distributed by Tripos, Inc., 1699 S. Hanley Rd., St. Louis MO 63144 USA, http:\/\/www.tripos.com"},{"key":"9082_CR24","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1021\/jm00350a003","volume":"25","author":"AK Ghose","year":"1982","unstructured":"Ghose AK, Crippen GM (1982) J Med Chem 25:892","journal-title":"J Med Chem"},{"key":"9082_CR25","unstructured":"SYBYL\u00ae is distributed by Tripos, Inc., 1699 S. Hanley Rd., St. Louis MO 63144 USA, http:\/\/www.tripos.com"},{"key":"9082_CR26","unstructured":"It should be noted in passing the N\n                  \n                    1\n                  -H tautomers given on the Research Collaboratory for Structural Bioinformatics (RCSB) web site (http:\/\/www.pdbbeta.rcsb.org\/pdb\/Welcome.do) for folate (1) and 5-deazafolate (2) would yield a grossly incorrect alignment if taken literally and used in place of the N\n                  \n                    3\n                  -H tautomers shown in Fig.\u00a03. The exact choice of tautomer provided to the program may affect the hydrogen bonding strength (gasp weight) assigned to each feature, but will generally have little or no qualitative effect on the models produced"},{"key":"9082_CR27","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1007\/s10822-004-5523-7","volume":"18","author":"SJ Cottrell","year":"2004","unstructured":"Cottrell SJ, Gillet VJ, Taylor R, Wilton DJ (2004) J Comput Aided Mol Des 18:665","journal-title":"J Comput Aided Mol Des"},{"key":"9082_CR28","unstructured":"Under the macro definitions used by default here and in SYBYL 7.2, anilinic nitrogens in general are recognized as both acceptor and donor atoms. This reflects that fact that the pK\n                  a of anilines can fall above or below physiological pH values, depending on exactly how they are substituted. Modifying the macro definitions to account for the fact that the exo nitrogens in aminopterins are not basic has no affect on the results shown in Fig.\u00a03 aside from the disappearance of A3 from the model query"},{"key":"9082_CR29","unstructured":"Note that 3\n                  N in 18 is \u201cseen\u201d as both a donor and an acceptor by GALAHAD, because of the potential for tautomerization with 1\n                  NH"},{"key":"9082_CR30","unstructured":"Langer, T (2005) Fifth European Workshop in Drug Design, Siena, Italy, 29 May\u20135 June 2005, http:\/\/www.unisi.it\/EWDD, http:\/\/www.inteligand.com\/demos\/cdk2-workshop-siena.pdf"},{"key":"9082_CR31","doi-asserted-by":"publisher","first-page":"567","DOI":"10.2174\/1381612013397843","volume":"7","author":"JS Mason","year":"2001","unstructured":"Mason JS, Good AC, Martin EJ (2001) Curr Pharm Des 7:567","journal-title":"Curr Pharm Des"},{"key":"9082_CR32","unstructured":"Shepphird JK, Clark RD (2006) J Comput Aided Mol Design (in press)"},{"key":"9082_CR33","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1002\/prot.20497","volume":"60","author":"JC Cole","year":"2005","unstructured":"Cole JC, Murray CW, Nissink JW, Taylor RD, Taylor R (2005) Proteins 60:325","journal-title":"Proteins"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-006-9082-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-006-9082-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-006-9082-y","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-006-9082-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T02:30:52Z","timestamp":1744165852000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-006-9082-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,9]]},"references-count":33,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2006,9]]}},"alternative-id":["9082"],"URL":"https:\/\/doi.org\/10.1007\/s10822-006-9082-y","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,9]]},"assertion":[{"value":"4 June 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 September 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 October 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}