{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T13:01:02Z","timestamp":1725973262027},"publisher-location":"New York, NY","reference-count":34,"publisher":"Springer New York","isbn-type":[{"type":"print","value":"9781493977550"},{"type":"electronic","value":"9781493977567"}],"license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018]]},"DOI":"10.1007\/978-1-4939-7756-7_7","type":"book-chapter","created":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T13:08:10Z","timestamp":1522242490000},"page":"105-121","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein\u2013Ligand Docking Method"],"prefix":"10.1007","author":[{"given":"Woong-Hee","family":"Shin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Kihara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,3,29]]},"reference":[{"issue":"4","key":"7_CR1","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/S1359-6446(97)01163-X","volume":"3","author":"WP Walters","year":"1998","unstructured":"Walters WP, Stahl MT, Murcko MA (1998) Virtual screening\u2014an overview. Drug Discov Today 3(4):160\u2013178","journal-title":"Drug Discov Today"},{"issue":"8","key":"7_CR2","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1021\/ci400206h","volume":"53","author":"J Schwartz","year":"2013","unstructured":"Schwartz J, Awale M, Reymond JL (2013) SMIfp (SMILES fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules. J Chem Info Model 53(8):1979\u20131989","journal-title":"J Chem Info Model"},{"issue":"6","key":"7_CR3","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1021\/ci010132r","volume":"42","author":"JL Durant","year":"2002","unstructured":"Durant JL, Leland BA, Henry DR, Nourse JG (2002) Reoptimization of MDL keys for use in drug discovery. J Chem Inf Comput Sci 42(6):1273\u20131280","journal-title":"J Chem Inf Comput Sci"},{"issue":"6","key":"7_CR4","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1093\/comjnl\/45.6.631","volume":"45","author":"JW Raymond","year":"2002","unstructured":"Raymond JW, Gardiner EJ, Willett P (2002) RASCAL: calculation of graph similarity using maximum common edge subgraphs. Comput J 45(6):631\u2013644","journal-title":"Comput J"},{"issue":"5","key":"7_CR5","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1021\/ci0498719","volume":"44","author":"A Bender","year":"2004","unstructured":"Bender A, Mussa HY, Glen RC (2004) Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J Chem Inf Comput Sci 44(5):1708\u20131718","journal-title":"J Chem Inf Comput Sci"},{"issue":"10","key":"7_CR6","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1002\/jcc.20681","volume":"28","author":"PJ Ballester","year":"2007","unstructured":"Ballester PJ, Richards WG (2007) Ultrafast shape recognition to search compound databases for similar molecular shapes. J Comput Chem 28(10):1711\u20131723","journal-title":"J Comput Chem"},{"issue":"1","key":"7_CR7","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1021\/jm0603365","volume":"50","author":"PCD Hawkins","year":"2007","unstructured":"Hawkins PCD, Skillman AG, Nicholls A (2007) Comparison of shape-matching and docking as virtual screening tools. J Med Chem 50(1):74\u201382","journal-title":"J Med Chem"},{"issue":"5","key":"7_CR8","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s10822-007-9114-2","volume":"21","author":"AN Jain","year":"2007","unstructured":"Jain AN (2007) Surflex-dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput-Aided Mol Des 21(5):281\u2013306","journal-title":"J Comput-Aided Mol Des"},{"issue":"2","key":"7_CR9","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455\u2013461","journal-title":"J Comput Chem"},{"issue":"15","key":"7_CR10","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1002\/jcc.23905","volume":"36","author":"WJ Allen","year":"2015","unstructured":"Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakus DT, Lang PT, Case DA, Kuntz ID, Rizzo RC (2015) DOCK 6: impact of new features and current docking performance. J Comput Chem 36(15):1132\u20131156","journal-title":"J Comput Chem"},{"issue":"2","key":"7_CR11","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1021\/jm900817u","volume":"53","author":"AR Leach","year":"2010","unstructured":"Leach AR, Gillet VJ, Lewis RA, Taylor R (2010) Three-dimensional pharmacophore methods in drug discovery. J Med Chem 53(2):539\u2013558","journal-title":"J Med Chem"},{"issue":"1","key":"7_CR12","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1021\/ci049885e","volume":"45","author":"G Wolber","year":"2005","unstructured":"Wolber G, Langer T (2005) LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Info Model 45(1):160\u2013169","journal-title":"J Chem Info Model"},{"issue":"9","key":"7_CR13","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1021\/acs.jcim.6b00163","volume":"56","author":"WH Shin","year":"2016","unstructured":"Shin WH, Christoffer CW, Wang J, Kihara D (2016) PL-PatchSurfer2: improved local surface matching-based virtual screening method that is tolerant to target and ligand structure variation. J Chem Info Model 56(9):1676\u20131691","journal-title":"J Chem Info Model"},{"doi-asserted-by":"crossref","unstructured":"Novotni M, Klein R (2003) 3D Zernike descriptors for content based shape retrieval. In: Proceedings of eighth ACM symposium on solid modeling and applications, Washington, pp 216\u2013225","key":"7_CR14","DOI":"10.1145\/781606.781639"},{"issue":"7","key":"7_CR15","doi-asserted-by":"crossref","first-page":"12841","DOI":"10.3390\/molecules200712841","volume":"20","author":"WH Shin","year":"2015","unstructured":"Shin WH, Zhu X, Bures MG, Kihara D (2015) Three-dimensional compound comparison methods and their application in drug discovery. Molecules 20(7):12841\u201312962","journal-title":"Molecules"},{"issue":"5","key":"7_CR16","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1093\/bioinformatics\/btu724","volume":"31","author":"X Zhu","year":"2015","unstructured":"Zhu X, Xiong Y, Kihara D (2015) Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. Bioinformatics 31(5):707\u2013713","journal-title":"Bioinformatics"},{"key":"7_CR17","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1186\/s12859-015-0580-6","volume":"16","author":"J Esquivel-Rodriguez","year":"2015","unstructured":"Esquivel-Rodriguez J, Xiong Y, Han X, Gang S, Christoffer CW, Kihara D (2015) Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinf 16:181","journal-title":"BMC Bioinf"},{"key":"7_CR18","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1186\/1471-2105-10-407","volume":"10","author":"V Venkatraman","year":"2009","unstructured":"Venkatraman V, Yang YD, Sael L, Kihara D (2009) Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinf 10:407","journal-title":"BMC Bioinf"},{"issue":"18","key":"7_CR19","doi-asserted-by":"crossref","first-page":"10037","DOI":"10.1073\/pnas.181342398","volume":"98","author":"NA Baker","year":"2001","unstructured":"Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98(18):10037\u201310041","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"7_CR20","doi-asserted-by":"crossref","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 (2010) Conformer generation with OMEGA: algorithm and validation using high quality structures from the protein databank and Cambridge Structural Database. J Chem Info Model 50(4):572\u2013584","journal-title":"J Chem Info Model"},{"issue":"4","key":"7_CR21","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1002\/prot.24018","volume":"80","author":"L Sael","year":"2012","unstructured":"Sael L, Kihara D (2012) Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. Proteins 80(4):1177\u20131185","journal-title":"Proteins"},{"issue":"6","key":"7_CR22","doi-asserted-by":"crossref","first-page":"2140","DOI":"10.1021\/ci700257y","volume":"47","author":"T Cheng","year":"2007","unstructured":"Cheng T, Zhao Y, Li X, Lin F, Xu Y, Zhang X, Li Y, Wang R (2007) Computation of octanol\u2212water partition coefficients by guiding an additive model with knowledge. J Chem Info Model 47(6):2140\u20132148","journal-title":"J Chem Info Model"},{"issue":"5","key":"7_CR23","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1007\/BF00124359","volume":"7","author":"W Heiden","year":"1993","unstructured":"Heiden W, Moeckel G, Brickmann J (1993) A new approach to analysis and display of local lipophilicity\/hydrophilicity mapped on molecular surfaces. J Comput-Aided Mol Des 7(5):503\u2013514","journal-title":"J Comput-Aided Mol Des"},{"key":"7_CR24","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","volume":"3","author":"NM O\u2019Boyle","year":"2011","unstructured":"O\u2019Boyle NM, Banck M, James CA, Morley C, Vandermeersh T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminf 3:33","journal-title":"J Cheminf"},{"issue":"13","key":"7_CR25","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605\u20131612","journal-title":"J Comput Chem"},{"issue":"2","key":"7_CR26","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1002\/prot.21732","volume":"71","author":"B Li","year":"2008","unstructured":"Li B, Turuvekere S, Agrawal M, La D, Ramani K, Kihara D (2008) Characterization of local geometry of protein surfaces with the visibility criterion. Proteins 71(2):670\u2013683","journal-title":"Proteins"},{"issue":"7","key":"7_CR27","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1021\/ci3001277","volume":"52","author":"JJ Irwin","year":"2012","unstructured":"Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman E (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52(7):1757\u20131768","journal-title":"J Chem Inf Model"},{"issue":"D1","key":"7_CR28","doi-asserted-by":"crossref","first-page":"D1083","DOI":"10.1093\/nar\/gkt1031","volume":"42","author":"AP Bento","year":"2014","unstructured":"Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Kr\u00fcger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Res 42(D1):D1083\u2013D1090","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"7_CR29","doi-asserted-by":"crossref","first-page":"D1202","DOI":"10.1093\/nar\/gkv951","volume":"44","author":"S Kim","year":"2016","unstructured":"Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH (2016) PubChem substance and compound databases. Nucleic Acids Res 44(D1):D1202\u2013D1213","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"7_CR30","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/S1056-8719(00)00107-6","volume":"44","author":"CA Lipinski","year":"2000","unstructured":"Lipinski CA (2000) Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 44(1):235\u2013249","journal-title":"J Pharmacol Toxicol Methods"},{"issue":"3","key":"7_CR31","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1021\/ci000150t","volume":"41","author":"JH Volgt","year":"2001","unstructured":"Volgt JH, Blenfalt B, Wang S, Nicklaus MC (2001) Comparison of the NCI open database with seven large chemical structural databases. J Chem Inf Comput Sci 41(3):702\u2013712","journal-title":"J Chem Inf Comput Sci"},{"issue":"7","key":"7_CR32","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1634\/theoncologist.2009-0009","volume":"14","author":"DL Wheeler","year":"2009","unstructured":"Wheeler DL, Iida M, Dunn EF (2009) The role of Src in solid tumors. Oncologist 14(7):667\u2013678","journal-title":"Oncologist"},{"issue":"2","key":"7_CR33","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1139\/o03-077","volume":"82","author":"SM Dehm","year":"2004","unstructured":"Dehm SM, Bonham K (2004) SRC gene expression in human cancer: the role of transcriptional activation. Biochem Cell Biol 82(2):263\u2013274","journal-title":"Biochem Cell Biol"},{"issue":"23","key":"7_CR34","doi-asserted-by":"crossref","first-page":"6789","DOI":"10.1021\/jm0608356","volume":"49","author":"N Huang","year":"2006","unstructured":"Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49(23):6789\u20136801","journal-title":"J Med Chem"}],"container-title":["Methods in Molecular Biology","Computational Drug Discovery and Design"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-7756-7_7","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T11:48:38Z","timestamp":1719920918000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-4939-7756-7_7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018]]},"ISBN":["9781493977550","9781493977567"],"references-count":34,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-7756-7_7","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"type":"print","value":"1064-3745"},{"type":"electronic","value":"1940-6029"}],"subject":[],"published":{"date-parts":[[2018]]}}}