{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,19]],"date-time":"2024-03-19T09:16:53Z","timestamp":1710839813425},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,11,7]],"date-time":"2012-11-07T00:00:00Z","timestamp":1352246400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D) descriptions to the small-molecule records contained in the PubChem Compound database and provides various search and analysis tools that exploit 3-D molecular similarity. Therefore, the efficient use of PubChem3D resources requires an understanding of the statistical and biological meaning of computed 3-D molecular similarity scores between molecules.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The present study investigated effects of employing multiple conformers per compound upon the 3-D similarity scores between ten thousand randomly selected biologically-tested compounds (10-K set) and between non-inactive compounds in a given biological assay (156-K set). When the \u201cbest-conformer-pair\u201d approach, in which a 3-D similarity score between two compounds is represented by the greatest similarity score among all possible conformer pairs arising from a compound pair, was employed with ten diverse conformers per compound, the average 3-D similarity scores for the 10-K set increased by 0.11, 0.09, 0.15, 0.16, 0.07, and 0.18 for <jats:italic>ST<\/jats:italic>\n              <jats:sup>\n                <jats:italic>ST-opt<\/jats:italic>\n              <\/jats:sup>, <jats:italic>CT<\/jats:italic>\n              <jats:sup>\n                <jats:italic>ST-opt<\/jats:italic>\n              <\/jats:sup>, <jats:italic>ComboT<\/jats:italic>\n              <jats:sup>\n                <jats:italic>ST-opt<\/jats:italic>\n              <\/jats:sup>, <jats:italic>ST<\/jats:italic>\n              <jats:sup>\n                <jats:italic>CT-opt<\/jats:italic>\n              <\/jats:sup>, <jats:italic>CT<\/jats:italic>\n              <jats:sup>\n                <jats:italic>CT-opt<\/jats:italic>\n              <\/jats:sup>, and <jats:italic>ComboT<\/jats:italic>\n              <jats:sup>\n                <jats:italic>CT-opt<\/jats:italic>\n              <\/jats:sup>, respectively, relative to the corresponding averages computed using a single conformer per compound. Interestingly, the best-conformer-pair approach also increased the average 3-D similarity scores for the non-inactive\u2013non-inactive (NN) pairs for a given assay, by comparable amounts to those for the random compound pairs, although some assays showed a pronounced increase in the per-assay NN-pair 3-D similarity scores, compared to the average increase for the random compound pairs.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>These results suggest that the use of ten diverse conformers per compound in PubChem bioassay data analysis using 3-D molecular similarity is not expected to increase the separation of non-inactive from random and inactive spaces \u201con average\u201d, although some assays show a noticeable separation between the non-inactive and random spaces when multiple conformers are used for each compound. The present study is a critical next step to understand effects of conformational diversity of the molecules upon the 3-D molecular similarity and its application to biological activity data analysis in PubChem. The results of this study may be helpful to build search and analysis tools that exploit 3-D molecular similarity between compounds archived in PubChem and other molecular libraries in a more efficient way.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1758-2946-4-28","type":"journal-article","created":{"date-parts":[[2012,11,7]],"date-time":"2012-11-07T23:13:59Z","timestamp":1352330039000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis"],"prefix":"10.1186","volume":"4","author":[{"given":"Sunghwan","family":"Kim","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evan E","family":"Bolton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen H","family":"Bryant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,11,7]]},"reference":[{"key":"346_CR1","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/S1574-1400(08)00012-1","volume-title":"Annual Reports in Computational Chemistry. Volume 4","author":"EE Bolton","year":"2008","unstructured":"Bolton EE, Wang Y, Thiessen PA, Bryant SH: PubChem: integrated platform of small molecules and biological activities. Annual Reports in Computational Chemistry. Volume 4. Edited by: Ralph AW, David CS. 2008, Amsterdam, the Netherlands: Elsevier, 217-241."},{"key":"346_CR2","doi-asserted-by":"publisher","first-page":"D255","DOI":"10.1093\/nar\/gkp965","volume":"38","author":"YL Wang","year":"2010","unstructured":"Wang YL, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang JY, Xiao JW, Zhang J, Bryant SH: An overview of the PubChem BioAssay resource. Nucleic Acids Res. 2010, 38: D255-D266. 10.1093\/nar\/gkp965.","journal-title":"Nucleic Acids Res"},{"key":"346_CR3","doi-asserted-by":"publisher","first-page":"D400","DOI":"10.1093\/nar\/gkr1132","volume":"40","author":"YL Wang","year":"2012","unstructured":"Wang YL, Xiao JW, Suzek TO, Zhang J, Wang JY, Zhou ZG, Han LY, Karapetyan K, Dracheva S, Shoemaker BA, et al: PubChem's BioAssay Database. Nucleic Acids Res. 2012, 40: D400-D412. 10.1093\/nar\/gkr1132.","journal-title":"Nucleic Acids Res"},{"key":"346_CR4","doi-asserted-by":"publisher","first-page":"D13","DOI":"10.1093\/nar\/gkr1184","volume":"40","author":"EW Sayers","year":"2012","unstructured":"Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2012, 40: D13-D25. 10.1093\/nar\/gkr1184.","journal-title":"Nucleic Acids Res"},{"key":"346_CR5","unstructured":"PubChem3D Thematic Series. http:\/\/www.jcheminf.com\/series\/pubchem3d,"},{"key":"346_CR6","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1758-2946-3-4","volume":"3","author":"EE Bolton","year":"2011","unstructured":"Bolton EE, Kim S, Bryant SH: PubChem3D: conformer generation. J Cheminform. 2011, 3: 4-10.1186\/1758-2946-3-4.","journal-title":"J Cheminform"},{"key":"346_CR7","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/1758-2946-3-9","volume":"3","author":"EE Bolton","year":"2011","unstructured":"Bolton EE, Kim S, Bryant SH: PubChem3D: diversity of shape. J Cheminform. 2011, 3: 9-10.1186\/1758-2946-3-9.","journal-title":"J Cheminform"},{"key":"346_CR8","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1758-2946-3-13","volume":"3","author":"EE Bolton","year":"2011","unstructured":"Bolton EE, Kim S, Bryant SH: PubChem3D: similar conformers. J Cheminform. 2011, 3: 13-10.1186\/1758-2946-3-13.","journal-title":"J Cheminform"},{"key":"346_CR9","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1758-2946-3-25","volume":"3","author":"S Kim","year":"2011","unstructured":"Kim S, Bolton EE, Bryant SH: PubChem3D: shape compatibility filtering using molecular shape quadrupoles. J Cheminform. 2011, 3: 25-10.1186\/1758-2946-3-25.","journal-title":"J Cheminform"},{"key":"346_CR10","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1758-2946-3-26","volume":"3","author":"S Kim","year":"2011","unstructured":"Kim S, Bolton EE, Bryant SH: PubChem3D: biologically relevant 3-D similarity. J Cheminform. 2011, 3: 26-10.1186\/1758-2946-3-26.","journal-title":"J Cheminform"},{"key":"346_CR11","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/1758-2946-3-32","volume":"3","author":"EE Bolton","year":"2011","unstructured":"Bolton EE, Chen J, Kim S, Han L, He S, Shi W, Simonyan V, Sun Y, Thiessen PA, Wang J, et al: PubChem3D: a new resource for scientists. J Cheminform. 2011, 3: 32-10.1186\/1758-2946-3-32.","journal-title":"J Cheminform"},{"key":"346_CR12","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1021\/ci200528d","volume":"52","author":"T Scior","year":"2012","unstructured":"Scior T, Bender A, Tresadern G, Medina-Franco JL, Martinez-Mayorga K, Langer T, Cuanalo-Contreras K, Agrafiotis DK: Recognizing pitfalls in virtual screening: a critical review. J Chem Inf Model. 2012, 52: 867-881. 10.1021\/ci200528d.","journal-title":"J Chem Inf Model"},{"key":"346_CR13","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1016\/S1093-3263(02)00204-8","volume":"21","author":"J Bostrom","year":"2003","unstructured":"Bostrom J, Greenwood JR, Gottfries J: Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model. 2003, 21: 449-462. 10.1016\/S1093-3263(02)00204-8.","journal-title":"J Mol Graph Model"},{"key":"346_CR14","doi-asserted-by":"publisher","first-page":"1489","DOI":"10.1021\/jm040163o","volume":"48","author":"TS Rush","year":"2005","unstructured":"Rush TS, Grant JA, Mosyak L, Nicholls A: A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem. 2005, 48: 1489-1495. 10.1021\/jm040163o.","journal-title":"J Med Chem"},{"key":"346_CR15","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: 74-82. 10.1021\/jm0603365.","journal-title":"J Med Chem"},{"key":"346_CR16","doi-asserted-by":"publisher","first-page":"1504","DOI":"10.1021\/ci700052x","volume":"47","author":"GB McGaughey","year":"2007","unstructured":"McGaughey GB, Sheridan RP, Bayly CI, Culberson JC, Kreatsoulas C, Lindsley S, Maiorov V, Truchon JF, Cornell WD: Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model. 2007, 47: 1504-1519. 10.1021\/ci700052x.","journal-title":"J Chem Inf Model"},{"key":"346_CR17","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1007\/s10822-008-9168-9","volume":"22","author":"RP Sheridan","year":"2008","unstructured":"Sheridan RP, McGaughey GB, Cornell WD: Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results. J Comput Aided Mol Des. 2008, 22: 257-265. 10.1007\/s10822-008-9168-9.","journal-title":"J Comput Aided Mol Des"},{"key":"346_CR18","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1021\/ci7004498","volume":"48","author":"SW Muchmore","year":"2008","unstructured":"Muchmore SW, Debe DA, Metz JT, Brown SP, Martin YC, Hajduk PJ: Application of belief theory to similarity data fusion for use in analog searching and lead hopping. J Chem Inf Model. 2008, 48: 941-948. 10.1021\/ci7004498.","journal-title":"J Chem Inf Model"},{"key":"346_CR19","unstructured":"ROCS - Rapid Overlay of Chemical Structures, Version 3.0.0. 2009, Santa Fe, NM: OpenEye Scientific Software, Inc"},{"key":"346_CR20","volume-title":"C++, Version 1.8.0","author":"TK Shape","year":"2010","unstructured":"Shape TK: C++, Version 1.8.0. 2010, Santa Fe, NM: OpenEye Scientific Software, Inc"},{"key":"346_CR21","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1002\/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K","volume":"17","author":"JA Grant","year":"1996","unstructured":"Grant JA, Gallardo MA, Pickup BT: A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape. J Comput Chem. 1996, 17: 1653-1666. 10.1002\/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K.","journal-title":"J Comput Chem"},{"key":"346_CR22","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1021\/ci100031x","volume":"50","author":"PCD Hawkins","year":"2010","unstructured":"Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT: Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model. 2010, 50: 572-584. 10.1021\/ci100031x.","journal-title":"J Chem Inf Model"},{"key":"346_CR23","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1021\/ci00067a016","volume":"30","author":"NW Murrall","year":"1990","unstructured":"Murrall NW, Davies EK: Conformational freedom in 3-D databases. 1. Techniques. J Chem Inf Comput Sci. 1990, 30: 312-316. 10.1021\/ci00067a016.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR24","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1021\/ci00017a025","volume":"34","author":"T Hurst","year":"1994","unstructured":"Hurst T: Flexible 3D searching: the directed tweak technique. J Chem Inf Comput Sci. 1994, 34: 190-196. 10.1021\/ci00017a025.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR25","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1007\/BF00123667","volume":"8","author":"G Klebe","year":"1994","unstructured":"Klebe G, Mietzner T: A fast and efficient method to generate biologically relevant conformations. J Comput Aided Mol Des. 1994, 8: 583-606. 10.1007\/BF00123667.","journal-title":"J Comput Aided Mol Des"},{"key":"346_CR26","doi-asserted-by":"publisher","first-page":"2324","DOI":"10.1021\/ci050075s","volume":"46","author":"S Renner","year":"2006","unstructured":"Renner S, Schwab CH, Gasteiger J, Schneider G: Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors. J Chem Inf Model. 2006, 46: 2324-2332. 10.1021\/ci050075s.","journal-title":"J Chem Inf Model"},{"key":"346_CR27","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1021\/ci00022a012","volume":"34","author":"J Greene","year":"1994","unstructured":"Greene J, Kahn S, Savoj H, Sprague P, Teig S: Chemical function queries for 3D database search. J Chem Inf Comput Sci. 1994, 34: 1297-1308. 10.1021\/ci00022a012.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR28","doi-asserted-by":"publisher","first-page":"1848","DOI":"10.1021\/ci060084g","volume":"46","author":"J Kirchmair","year":"2006","unstructured":"Kirchmair J, Wolber G, Laggner C, Langer T: Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations. J Chem Inf Model. 2006, 46: 1848-1861. 10.1021\/ci060084g.","journal-title":"J Chem Inf Model"},{"key":"346_CR29","doi-asserted-by":"publisher","first-page":"1428","DOI":"10.1021\/ci7000956","volume":"47","author":"YV Borodina","year":"2007","unstructured":"Borodina YV, Bolton E, Fontaine F, Bryant SH: Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. J Chem Inf Model. 2007, 47: 1428-1437. 10.1021\/ci7000956.","journal-title":"J Chem Inf Model"},{"key":"346_CR30","doi-asserted-by":"publisher","first-page":"2305","DOI":"10.1021\/ci060042s","volume":"46","author":"J Sadowski","year":"2006","unstructured":"Sadowski J, Bostrom J: MIMUMBA revisited: Torsion angle rules for conformer generation derived from X-ray structures. J Chem Inf Model. 2006, 46: 2305-2309. 10.1021\/ci060042s.","journal-title":"J Chem Inf Model"},{"key":"346_CR31","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1023\/A:1015930826903","volume":"15","author":"J Bostrom","year":"2001","unstructured":"Bostrom J: Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J Comput Aided Mol Des. 2001, 15: 1137-1152. 10.1023\/A:1015930826903.","journal-title":"J Comput Aided Mol Des"},{"key":"346_CR32","doi-asserted-by":"publisher","first-page":"2182","DOI":"10.1021\/ci700024q","volume":"47","author":"J Kirchmair","year":"2007","unstructured":"Kirchmair J, Ristic S, Eder K, Markt P, Wolber G, Laggner C, Langer T: Fast and efficient in silico 3D screening: Toward maximum computational efficiency of pharmacophore-based and shape-based approaches. J Chem Inf Model. 2007, 47: 2182-2196. 10.1021\/ci700024q.","journal-title":"J Chem Inf Model"},{"key":"346_CR33","doi-asserted-by":"publisher","first-page":"2326","DOI":"10.1021\/ci800234q","volume":"48","author":"PC Fox","year":"2008","unstructured":"Fox PC, Wolohan PRN, Abrahamian E, Clark RD: Parameterization and conformational sampling effects in pharmacophore multiplet searching. J Chem Inf Model. 2008, 48: 2326-2334. 10.1021\/ci800234q.","journal-title":"J Chem Inf Model"},{"key":"346_CR34","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.2174\/0929867013372481","volume":"8","author":"Y Kurogi","year":"2001","unstructured":"Kurogi Y, Guner OF: Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr Med Chem. 2001, 8: 1035-1055. 10.2174\/0929867013372481.","journal-title":"Curr Med Chem"},{"key":"346_CR35","doi-asserted-by":"publisher","first-page":"2991","DOI":"10.2174\/0929867043364036","volume":"11","author":"O Guner","year":"2004","unstructured":"Guner O, Clement O, Kurogi Y: Pharmacophore modeling and three dimensional database searching for drug design using catalyst: recent advances. Curr Med Chem. 2004, 11: 2991-3005. 10.2174\/0929867043364036.","journal-title":"Curr Med Chem"},{"key":"346_CR36","unstructured":"PubChem substructure fingerprint description. [ftp:\/\/ftp.ncbi.nlm.nih.gov\/pubchem\/specifications\/pubchem_fingerprints.pdf]"},{"key":"346_CR37","doi-asserted-by":"publisher","first-page":"155","DOI":"10.2174\/1386207024607338","volume":"5","author":"JD Holliday","year":"2002","unstructured":"Holliday JD, Hu CY, Willett P: Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings. Combinatorial Chemistry & High Throughput Screening. 2002, 5: 155-166.","journal-title":"Combinatorial Chemistry & High Throughput Screening"},{"key":"346_CR38","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1021\/ci034001x","volume":"43","author":"JD Holliday","year":"2003","unstructured":"Holliday JD, Salim N, Whittle M, Willett P: Analysis and display of the size dependence of chemical similarity coefficients. J Chem Inf Comput Sci. 2003, 43: 819-828. 10.1021\/ci034001x.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR39","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ci025596j","volume":"43","author":"N Salim","year":"2003","unstructured":"Salim N, Holliday J, Willett P: Combination of fingerprint-based similarity coefficients using data fusion. J Chem Inf Comput Sci. 2003, 43: 435-442. 10.1021\/ci025596j.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR40","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.1021\/ci025531g","volume":"42","author":"X Chen","year":"2002","unstructured":"Chen X, Reynolds CH: Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients. J Chem Inf Comput Sci. 2002, 42: 1407-1414. 10.1021\/ci025531g.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR41","doi-asserted-by":"publisher","first-page":"6777","DOI":"10.1021\/jm049501b","volume":"47","author":"RD Cramer","year":"2004","unstructured":"Cramer RD, Jilek RJ, Guessregen S, Clark SJ, Wendt B, Clark RD: \u201cLead hopping\u201d. Validation of topomer similarity as a superior predictor of similar biological activities. J Med Chem. 2004, 47: 6777-6791. 10.1021\/jm049501b.","journal-title":"J Med Chem"},{"key":"346_CR42","doi-asserted-by":"publisher","first-page":"3563","DOI":"10.1021\/jm010036h","volume":"44","author":"GM Makara","year":"2001","unstructured":"Makara GM: Measuring molecular similarity and diversity: total pharmacophore diversity. J Med Chem. 2001, 44: 3563-3571. 10.1021\/jm010036h.","journal-title":"J Med Chem"},{"key":"346_CR43","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1007\/s10822-004-4067-1","volume":"18","author":"AC Good","year":"2004","unstructured":"Good AC, Hermsmeier MA, Hindle SA: Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments. J Comput Aided Mol Des. 2004, 18: 529-536. 10.1007\/s10822-004-4067-1.","journal-title":"J Comput Aided Mol Des"},{"key":"346_CR44","doi-asserted-by":"publisher","first-page":"6144","DOI":"10.1021\/jm049654z","volume":"47","author":"JL Jenkins","year":"2004","unstructured":"Jenkins JL, Glick M, Davies JW: A 3D similarity method for scaffold hopping from the known drugs or natural ligands to new chemotypes. J Med Chem. 2004, 47: 6144-6159. 10.1021\/jm049654z.","journal-title":"J Med Chem"},{"key":"346_CR45","unstructured":"National Center for Biotechnology Information. PubChem BioAssay Database; AID=1033, Source=Sanford-Burnham Center for Chemical Genomics. http:\/\/pubchem.ncbi.nlm.nih.gov\/assay\/assay.cgi?aid=1033 (accessed Mar. 16, 2012)"},{"key":"346_CR46","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1038\/74062","volume":"7","author":"M Pellecchia","year":"2000","unstructured":"Pellecchia M, Montgomery DL, Stevens SY, Vander Kooi CW, Feng HP, Gierasch LM, Zuiderweg ERP: Structural insights into substrate binding by the molecular chaperone DnaK. Nat Struct Biol. 2000, 7: 298-303. 10.1038\/74062.","journal-title":"Nat Struct Biol"},{"key":"346_CR47","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/j.cell.2006.04.014","volume":"125","author":"B Bukau","year":"2006","unstructured":"Bukau B, Weissman J, Horwich A: Molecular chaperones and protein quality control. Cell. 2006, 125: 443-451. 10.1016\/j.cell.2006.04.014.","journal-title":"Cell"},{"key":"346_CR48","unstructured":"National Center for Biotechnology Information. PubChem BioAssay Database; AID=491, Source=BindingDB. http:\/\/pubchem.ncbi.nlm.nih.gov\/assay\/assay.cgi?aid=491 (accessed Mar. 16, 2012)"},{"key":"346_CR49","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1021\/jm970374b","volume":"41","author":"PW Smith","year":"1998","unstructured":"Smith PW, Sollis SL, Howes PD, Cherry PC, Starkey ID, Cobley KN, Weston H, Scicinski J, Merritt A, Whittington A, et al: Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 1. Discovery, synthesis, biological activity, and structure-activity relationships of 4-guanidino- and 4-amino-4H-pyran-6-carboxamides. J Med Chem. 1998, 41: 787-797. 10.1021\/jm970374b.","journal-title":"J Med Chem"},{"key":"346_CR50","doi-asserted-by":"publisher","first-page":"4379","DOI":"10.1021\/jm010277p","volume":"44","author":"P Chand","year":"2001","unstructured":"Chand P, Kotian PL, Dehghani A, El-Kattan Y, Lin TH, Hutchison TL, Babu YS, Bantia S, Elliott AJ, Montgomery JA: Systematic structure-based design and stereoselective synthesis of novel multisubstituted cyclopentane derivatives with potent antiinfluenza activity. J Med Chem. 2001, 44: 4379-4392. 10.1021\/jm010277p.","journal-title":"J Med Chem"},{"key":"346_CR51","volume-title":"Concepts and Applications of Molecular Similarity","author":"MA Johnson","year":"1990","unstructured":"Johnson MA, Maggiora GM: Concepts and Applications of Molecular Similarity. 1990, New York, NY: John Wiley & Sons, Inc"},{"key":"346_CR52","doi-asserted-by":"publisher","first-page":"1816","DOI":"10.1021\/ci049920h","volume":"44","author":"M Thimm","year":"2004","unstructured":"Thimm M, Goede A, Hougardy S, Preissner R: Comparison of 2D similarity and 3D superposition. application to searching a conformational drug database. J Chem Inf Comput Sci. 2004, 44: 1816-1822. 10.1021\/ci049920h.","journal-title":"J Chem Inf Comput Sci"},{"key":"346_CR53","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1021\/ci800249s","volume":"49","author":"A Bender","year":"2009","unstructured":"Bender A, Jenkins JL, Scheiber J, Sukuru SCK, Glick M, Davies JW: How similar are similarity searching methods? a principal component analysis of molecular descriptor space. J Chem Inf Model. 2009, 49: 108-119. 10.1021\/ci800249s.","journal-title":"J Chem Inf Model"},{"key":"346_CR54","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1021\/jm030520f","volume":"47","author":"AN Jain","year":"2004","unstructured":"Jain AN: Ligand-based structural hypotheses for virtual screening. J Med Chem. 2004, 47: 947-961. 10.1021\/jm030520f.","journal-title":"J Med Chem"},{"key":"346_CR55","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1021\/ci050348j","volume":"46","author":"J Hert","year":"2006","unstructured":"Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A: New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching. J Chem Inf Model. 2006, 46: 462-470. 10.1021\/ci050348j.","journal-title":"J Chem Inf Model"},{"key":"346_CR56","volume-title":"J Cheminform","author":"S Kim","year":"2012","unstructured":"Kim S, Bolton EE, Bryant SH: PubChem3D: conformer ensemble accuracy. J Cheminform. 2012, submitted for publication"},{"key":"346_CR57","doi-asserted-by":"publisher","first-page":"3222","DOI":"10.1021\/jm8001058","volume":"51","author":"J Venhorst","year":"2008","unstructured":"Venhorst J, Nunez S, Terpstra JW, Kruse CG: Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints. J Med Chem. 2008, 51: 3222-3229. 10.1021\/jm8001058.","journal-title":"J Med Chem"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1758-2946-4-28.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1758-2946-4-28\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1758-2946-4-28.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T21:12:34Z","timestamp":1630530754000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/1758-2946-4-28"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,7]]},"references-count":57,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["346"],"URL":"https:\/\/doi.org\/10.1186\/1758-2946-4-28","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,11,7]]},"assertion":[{"value":"28 June 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 October 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 November 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"28"}}