{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,21]],"date-time":"2025-09-21T16:57:40Z","timestamp":1758473860377},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"S16","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-s16-s5","type":"journal-article","created":{"date-parts":[[2014,12,8]],"date-time":"2014-12-08T12:03:10Z","timestamp":1418040190000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Combining spatial and chemical information for clustering pharmacophores"],"prefix":"10.1186","volume":"15","author":[{"given":"Lingxiao","family":"Zhou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renate","family":"Griffith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruno","family":"Gaeta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,12,8]]},"reference":[{"issue":"2","key":"6738_CR1","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1021\/jm900817u","volume":"53","author":"AR Leach","year":"2010","unstructured":"Leach AR, Gillet VJ, Lewis RA, Taylor R: Three-Dimensional Pharmacophore Methods in Drug Discovery. J Med Chem. 2010, 53 (2): 539-558. 10.1021\/jm900817u.","journal-title":"J Med Chem"},{"issue":"5","key":"6738_CR2","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1351\/pac199870051129","volume":"70","author":"G Wermuth","year":"1998","unstructured":"Wermuth G, Ganellin CR, Lindberg P, Mitscher LA: Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure Appl Chem. 1998, 70 (5): 1129-1143.","journal-title":"Pure Appl Chem"},{"issue":"3","key":"6738_CR3","doi-asserted-by":"publisher","first-page":"173","DOI":"10.2174\/157340911796504305","volume":"7","author":"J Sutter","year":"2011","unstructured":"Sutter J, Li JB, Maynard AJ, Goupil A, Luu T, Nadassy K: New Features that Improve the Pharmacophore Tools from Accelrys. Curr Comput-Aid Drug. 2011, 7 (3): 173-180. 10.2174\/157340911796504305.","journal-title":"Curr Comput-Aid Drug"},{"issue":"12","key":"6738_CR4","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1007\/s10822-006-9078-7","volume":"20","author":"G Wolber","year":"2006","unstructured":"Wolber G, Dornhofer AA, Langer T: Efficient overlay of small organic molecules using 3D pharmacophores. Journal of computer-aided molecular design. 2006, 20 (12): 773-788.","journal-title":"Journal of computer-aided molecular design"},{"issue":"W1","key":"6738_CR5","doi-asserted-by":"publisher","first-page":"W409","DOI":"10.1093\/nar\/gks378","volume":"40","author":"DR Koes","year":"2012","unstructured":"Koes DR, Camacho CJ: ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Res. 2012, 40 (W1): W409-W414. 10.1093\/nar\/gks378.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"6738_CR6","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1002\/wcms.1152","volume":"4","author":"JD MacCuish","year":"2014","unstructured":"MacCuish JD, MacCuish NE: Chemoinformatics applications of cluster analysis. Wires Comput Mol Sci. 2014, 4 (1): 34-48. 10.1002\/wcms.1152.","journal-title":"Wires Comput Mol Sci"},{"issue":"4","key":"6738_CR7","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1007\/BF00125178","volume":"9","author":"AC Good","year":"1995","unstructured":"Good AC, Kuntz ID: Investigating the Extension of Pairwise Distance Pharmacophore Measures to Triplet-Based Descriptors. Journal of computer-aided molecular design. 1995, 9 (4): 373-379. 10.1007\/BF00125178.","journal-title":"Journal of computer-aided molecular design"},{"key":"6738_CR8","first-page":"576","volume-title":"Pac Symp Biocomput","author":"JS Mason","year":"2000","unstructured":"Mason JS, Cheney DL: Library design and virtual screening using multiple 4-point pharmacophore fingerprints. Pac Symp Biocomput. 2000, 576-587."},{"issue":"2","key":"6738_CR9","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1111\/j.1469-8137.1912.tb05611.x","volume":"11","author":"P Jaccard","year":"1912","unstructured":"Jaccard P: The distribution of the flora in the alpine zone. New Phytologist. 1912, 11 (2): 37-50. 10.1111\/j.1469-8137.1912.tb05611.x.","journal-title":"New Phytologist"},{"issue":"1","key":"6738_CR10","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1021\/jm0603365","volume":"50","author":"PCD Hawkins","year":"2007","unstructured":"Hawkins PCD, Skillman AG, Nicholls A: Comparison of shape-matching and docking as virtual screening tools. J Med Chem. 2007, 50 (1): 74-82. 10.1021\/jm0603365.","journal-title":"J Med Chem"},{"issue":"3","key":"6738_CR11","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1145\/331499.331504","volume":"31","author":"AK Jain","year":"1999","unstructured":"Jain AK, Murty MN, Flynn PJ: Data clustering: A review. Acm Comput Surv. 1999, 31 (3): 264-323. 10.1145\/331499.331504.","journal-title":"Acm Comput Surv"},{"issue":"301","key":"6738_CR12","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1080\/01621459.1963.10500845","volume":"58","author":"JH Ward","year":"1963","unstructured":"Ward JH: Hierarchical Grouping to Optimize an Objective Function. J Am Stat Assoc. 1963, 58 (301): 236-&. 10.1080\/01621459.1963.10500845.","journal-title":"J Am Stat Assoc"},{"issue":"2-3","key":"6738_CR13","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/BF01908075","volume":"2","author":"L Hubert","year":"1985","unstructured":"Hubert L, Arabie P: Comparing Partitions. J Classif. 1985, 2 (2-3): 193-218.","journal-title":"J Classif"},{"issue":"2","key":"6738_CR14","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1109\/TPAMI.1979.4766909","volume":"1","author":"DL Davies","year":"1979","unstructured":"Davies DL, Bouldin DW: Cluster Separation Measure. Ieee T Pattern Anal. 1979, 1 (2): 224-227.","journal-title":"Ieee T Pattern Anal"},{"issue":"2","key":"6738_CR15","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1109\/34.121791","volume":"14","author":"PJ Besl","year":"1992","unstructured":"Besl PJ, Mckay ND: A Method for Registration of 3-D Shapes. Ieee T Pattern Anal. 1992, 14 (2): 239-256. 10.1109\/34.121791.","journal-title":"Ieee T Pattern Anal"},{"issue":"1-3","key":"6738_CR16","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.theochem.2005.02.030","volume":"727","author":"A Rodriguez","year":"2005","unstructured":"Rodriguez A, Tomas MS, Perez JJ, Rubio-Martinez J: Assessment of the performance of cluster analysis grouping using pharmacophores as molecular descriptors. J Mol Struc-Theochem. 2005, 727 (1-3): 81-87. 10.1016\/j.theochem.2005.02.030.","journal-title":"J Mol Struc-Theochem"},{"issue":"18","key":"6738_CR17","doi-asserted-by":"publisher","first-page":"5959","DOI":"10.1021\/ja00226a005","volume":"110","author":"RD Cramer","year":"1988","unstructured":"Cramer RD, Patterson DE, Bunce JD: Comparative Molecular-Field Analysis (Comfa) .1. Effect of Shape on Binding of Steroids to Carrier Proteins. J Am Chem Soc. 1988, 110 (18): 5959-5967. 10.1021\/ja00226a005.","journal-title":"J Am Chem Soc"},{"issue":"29","key":"6738_CR18","doi-asserted-by":"publisher","first-page":"7769","DOI":"10.1021\/ja00134a023","volume":"117","author":"M Wagener","year":"1995","unstructured":"Wagener M, Sadowski J, Gasteiger J: Autocorrelation of Molecular-Surface Properties for Modeling Corticosteroid-Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks. J Am Chem Soc. 1995, 117 (29): 7769-7775. 10.1021\/ja00134a023.","journal-title":"J Am Chem Soc"},{"issue":"1","key":"6738_CR19","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1021\/ci025602b","volume":"43","author":"P Bultinck","year":"2003","unstructured":"Bultinck P, Carbo-Dorca R: Molecular quantum similarity matrix based clustering of molecules using dendrograms. J Chem Inf Comp Sci. 2003, 43 (1): 170-177. 10.1021\/ci025602b.","journal-title":"J Chem Inf Comp Sci"},{"issue":"4","key":"6738_CR20","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1354\/vp.42-4-405","volume":"42","author":"JA Ramos-Vara","year":"2005","unstructured":"Ramos-Vara JA: Technical aspects of immunohistochemistry. Vet Pathol. 2005, 42 (4): 405-426. 10.1354\/vp.42-4-405.","journal-title":"Vet Pathol"},{"issue":"1","key":"6738_CR21","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28 (1): 235-242. 10.1093\/nar\/28.1.235.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"6738_CR22","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1093\/bioinformatics\/18.1.175","volume":"18","author":"LC Allcorn","year":"2002","unstructured":"Allcorn LC, Martin ACR: SACS - Self-maintaining database of antibody crystal structure information. Bioinformatics. 2002, 18 (1): 175-181. 10.1093\/bioinformatics\/18.1.175.","journal-title":"Bioinformatics"},{"key":"6738_CR23","volume-title":"Mol Syst Biol","author":"F Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li WZ, Lopez R, McWilliam H, Remmert M, Soding J: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011, 7:"},{"issue":"4","key":"6738_CR24","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1021\/ci00020a020","volume":"34","author":"D Rogers","year":"1994","unstructured":"Rogers D, Hopfinger AJ: Application of Genetic Function Approximation to Quantitative Structure-Activity-Relationships and Quantitative Structure-Property Relationships. J Chem Inf Comp Sci. 1994, 34 (4): 854-866. 10.1021\/ci00020a020.","journal-title":"J Chem Inf Comp Sci"},{"key":"6738_CR25","doi-asserted-by":"publisher","first-page":"2724","DOI":"10.1109\/ROBOT.1991.132043","volume":"1-3","author":"Y Chen","year":"1991","unstructured":"Chen Y, Medioni G: Object Modeling by Registration of Multiple Range Images. 1991 Ieee International Conference on Robotics and Automation. 1991, 1-3: 2724-2729.","journal-title":"1991 Ieee International Conference on Robotics and Automation"},{"issue":"3","key":"6738_CR26","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1007\/BF00991003","volume":"14","author":"SP Dandamudi","year":"1985","unstructured":"Dandamudi SP, Sorenson PG: An Empirical Performance Comparison of Some Variations of the K-D Tree and Bd Tree. Int J Comput Inf Sci. 1985, 14 (3): 135-159. 10.1007\/BF00991003.","journal-title":"Int J Comput Inf Sci"},{"issue":"18","key":"6738_CR27","doi-asserted-by":"publisher","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","volume":"97","author":"O Alter","year":"2000","unstructured":"Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA. 2000, 97 (18): 10101-10106. 10.1073\/pnas.97.18.10101.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"6738_CR28","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1002\/jcc.21095","volume":"30","author":"V Hahnke","year":"2009","unstructured":"Hahnke V, Hofmann B, Grgat T, Proschak E, Steinhilber D, Schneider G: PhAST: pharmacophore alignment search tool. Journal of computational chemistry. 2009, 30 (5): 761-771. 10.1002\/jcc.21095.","journal-title":"Journal of computational chemistry"},{"issue":"W1","key":"6738_CR29","doi-asserted-by":"publisher","first-page":"W573","DOI":"10.1093\/nar\/gks485","volume":"40","author":"B Alix","year":"2012","unstructured":"Alix B, Boubacar DA, Vladimir M: T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res. 2012, 40 (W1): W573-W579. 10.1093\/nar\/gks485.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"6738_CR30","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1080\/1359432X.2012.748189","volume":"23","author":"H Lohse-Bossenz","year":"2014","unstructured":"Lohse-Bossenz H, Kunina-Habenicht O, Kunter M: Estimating within-group agreement in small groups: A proposed adjustment for the average deviation index. Eur J Work Organ Psy. 2014, 23 (3): 456-468. 10.1080\/1359432X.2012.748189.","journal-title":"Eur J Work Organ Psy"},{"issue":"2","key":"6738_CR31","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1021\/ci980410v","volume":"39","author":"D Robert","year":"1999","unstructured":"Robert D, Amat L, Carbo-Dorca R: Three-dimensional quantitative structure-activity relationships from tuned molecular quantum similarity measures: Prediction of the corticosteroid-binding globulin binding affinity for a steroid family. J Chem Inf Comp Sci. 1999, 39 (2): 333-344. 10.1021\/ci980410v.","journal-title":"J Chem Inf Comp Sci"},{"issue":"22","key":"6738_CR32","doi-asserted-by":"publisher","first-page":"11862","DOI":"10.1128\/JVI.01604-09","volume":"83","author":"S Bryson","year":"2009","unstructured":"Bryson S, Julien JP, Hynes RC, Pai EF: Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-humanimmunodeficiency virus type 1 antibody 2F5: vaccine design implications. J Virol. 2009, 83 (22): 11862-11875. 10.1128\/JVI.01604-09.","journal-title":"J Virol"},{"issue":"5","key":"6738_CR33","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1038\/nsb0597-374","volume":"4","author":"AL Corper","year":"1997","unstructured":"Corper AL, Sohi MK, Bonagura VR, Steinitz M, Jefferis R, Feinstein A, Beale D, Taussig MJ, Sutton BJ: Structure of human IgM rheumatoid factor Fab bound to its autoantigen IgG Fc reveals a novel topology of antibody-antigen interaction. Nat Struct Biol. 1997, 4 (5): 374-381. 10.1038\/nsb0597-374.","journal-title":"Nat Struct Biol"},{"issue":"5924","key":"6738_CR34","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1126\/science.1171491","volume":"324","author":"DC Ekiert","year":"2009","unstructured":"Ekiert DC, Bhabha G, Elsliger MA, Friesen RHE, Jongeneelen M, Throsby M, Goudsmit J, Wilson IA: Antibody Recognition of a Highly Conserved Influenza Virus Epitope. Science. 2009, 324 (5924): 246-251. 10.1126\/science.1171491.","journal-title":"Science"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S16-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T01:43:25Z","timestamp":1548207805000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S16-S5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":34,"journal-issue":{"issue":"S16","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6738"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s16-s5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"8 December 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S5"}}