{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T06:54:56Z","timestamp":1774508096666,"version":"3.50.1"},"publisher-location":"Cham","reference-count":44,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783319212326","type":"print"},{"value":"9783319212333","type":"electronic"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"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":[[2015]]},"DOI":"10.1007\/978-3-319-21233-3_4","type":"book-chapter","created":{"date-parts":[[2015,7,27]],"date-time":"2015-07-27T16:30:47Z","timestamp":1438014647000},"page":"41-52","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features"],"prefix":"10.1007","author":[{"given":"Radoslav","family":"Kriv\u00e1k","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Hoksza","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,7,28]]},"reference":[{"issue":"6","key":"4_CR1","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1074\/mcp.M400159-MCP200","volume":"4","author":"J An","year":"2005","unstructured":"An, J., Totrov, M., Abagyan, R.: Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteomics 4(6), 752\u2013761 (2005)","journal-title":"Mol. Cell. Proteomics"},{"issue":"6","key":"4_CR2","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1002\/widm.1072","volume":"2","author":"AL Boulesteix","year":"2012","unstructured":"Boulesteix, A.L., Janitza, S., Kruppa, J., K-nig, I.R.: Overview of random forest methodology and practical guidance with emphasis on computational biology and bioinformatics. Wiley Interdisc. Rev. Data Min. Knowl. Discov. 2(6), 493\u2013507 (2012)","journal-title":"Wiley Interdisc. Rev. Data Min. Knowl. Discov."},{"issue":"1","key":"4_CR3","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman, L.: Random forests. Mach. Learn. 45(1), 5\u201332 (2001)","journal-title":"Mach. Learn."},{"issue":"1","key":"4_CR4","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1073\/pnas.0707684105","volume":"105","author":"M Brylinski","year":"2008","unstructured":"Brylinski, M., Skolnick, J.: A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. U.S.A 105(1), 129\u2013134 (2008)","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"issue":"12","key":"4_CR5","doi-asserted-by":"publisher","first-page":"e1000585","DOI":"10.1371\/journal.pcbi.1000585","volume":"5","author":"JA Capra","year":"2009","unstructured":"Capra, J.A., Laskowski, R.A., Thornton, J.M., Singh, M., Funkhouser, T.A.: Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure. PLoS Comput. Biol. 5(12), e1000585 (2009)","journal-title":"PLoS Comput. Biol."},{"issue":"5","key":"4_CR6","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1016\/j.str.2011.02.015","volume":"19","author":"K Chen","year":"2011","unstructured":"Chen, K., Mizianty, M., Gao, J., Kurgan, L.: A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds. Structure (London, England: 1993) 19(5), 613\u2013621 (2011)","journal-title":"Structure (London, England: 1993)"},{"issue":"15","key":"4_CR7","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-15-S15-S4","volume":"15","author":"P Chen","year":"2014","unstructured":"Chen, P., Huang, J.Z., Gao, X.: Ligandrfs: random forest ensemble to identify ligand-binding residues from sequence information alone. BMC Bioinform. 15(15), S4 (2014)","journal-title":"BMC Bioinform."},{"issue":"8","key":"4_CR8","doi-asserted-by":"publisher","first-page":"2287","DOI":"10.1021\/ci300184x","volume":"52","author":"J Desaphy","year":"2012","unstructured":"Desaphy, J., Azdimousa, K., Kellenberger, E., Rognan, D.: Comparison and druggability prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes. J. Chem. Inf. Model. 52(8), 2287\u20132299 (2012)","journal-title":"J. Chem. Inf. Model."},{"issue":"3","key":"4_CR9","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1002\/jcc.540160303","volume":"16","author":"F Eisenhaber","year":"1995","unstructured":"Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., Scharf, M.: The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comput. Chem. 16(3), 273\u2013284 (1995)","journal-title":"J. Comput. Chem."},{"issue":"23","key":"4_CR10","doi-asserted-by":"publisher","first-page":"3185","DOI":"10.1093\/bioinformatics\/btp562","volume":"25","author":"D Ghersi","year":"2009","unstructured":"Ghersi, D., Sanchez, R.: EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures. Bioinformatics (Oxford, England) 25(23), 3185\u20133186 (2009)","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"4","key":"4_CR11","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1021\/jm061277y","volume":"50","author":"M Hartshorn","year":"2007","unstructured":"Hartshorn, M., Verdonk, M., Chessari, G., Brewerton, S., Mooij, W., Mortenson, P., Murray, C.: Diverse, high-quality test set for the validation of protein-ligand docking performance. J. Med. Chem. 50(4), 726\u2013741 (2007)","journal-title":"J. Med. Chem."},{"key":"4_CR12","doi-asserted-by":"crossref","unstructured":"Hendlich, M., Rippmann, F., Barnickel, G.: LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model. 15(6), 359\u2013363, 389 (1997)","DOI":"10.1016\/S1093-3263(98)00002-3"},{"issue":"2","key":"4_CR13","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/jmr.984","volume":"23","author":"S Henrich","year":"2010","unstructured":"Henrich, S., Outi, S., Huang, B., Rippmann, F., Cruciani, G., Wade, R.: Computational approaches to identifying and characterizing protein binding sites for ligand design. J. Mol. Recogn. (JMR) 23(2), 209\u2013219 (2010)","journal-title":"J. Mol. Recogn. (JMR)"},{"issue":"4","key":"4_CR14","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1089\/omi.2009.0045","volume":"13","author":"B Huang","year":"2009","unstructured":"Huang, B.: MetaPocket: a meta approach to improve protein ligand binding site prediction. Omics J. Integr. Biol. 13(4), 325\u2013330 (2009)","journal-title":"Omics J. Integr. Biol."},{"issue":"1","key":"4_CR15","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1472-6807-6-19","volume":"6","author":"B Huang","year":"2006","unstructured":"Huang, B., Schroeder, M.: Ligsitecsc: predicting ligand binding sites using the connolly surface and degree of conservation. BMC Struct. Biol. 6(1), 19 (2006). http:\/\/www.biomedcentral.com\/1472-6807\/6\/19","journal-title":"BMC Struct. Biol."},{"key":"4_CR16","doi-asserted-by":"crossref","unstructured":"Kauffman, C., Karypis, G.: Librus: combined machine learning and homology information for sequence-based ligand-binding residue prediction. Bioinformatics (Oxford, England) 25(23), 3099\u20133107 (2009). http:\/\/bioinformatics.oxfordjournals.org\/cgi\/pmidlookup?view=long&pmid=19786483","DOI":"10.1093\/bioinformatics\/btp561"},{"issue":"11","key":"4_CR17","doi-asserted-by":"publisher","first-page":"e1003321","DOI":"10.1371\/journal.pcbi.1003321","volume":"9","author":"NA Khazanov","year":"2013","unstructured":"Khazanov, N.A., Carlson, H.A.: Exploring the composition of protein-ligand binding sites on a large scale. PLoS Comput. Biol. 9(11), e1003321 (2013)","journal-title":"PLoS Comput. Biol."},{"key":"4_CR18","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.sbi.2013.11.012","volume":"25","author":"J Konc","year":"2014","unstructured":"Konc, J., Janei, D.: Binding site comparison for function prediction and pharmaceutical discovery. Curr. Opin. Struct. Biol. 25, 34\u201339 (2014)","journal-title":"Curr. Opin. Struct. Biol."},{"issue":"1","key":"4_CR19","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13321-015-0059-5","volume":"7","author":"R Krivak","year":"2015","unstructured":"Krivak, R., Hoksza, D.: Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J. Cheminformatics 7(1), 12 (2015). http:\/\/www.jcheminf.com\/content\/7\/1\/12","journal-title":"J. Cheminformatics"},{"issue":"1","key":"4_CR20","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/0022-2836(82)90515-0","volume":"157","author":"J Kyte","year":"1982","unstructured":"Kyte, J., Doolittle, R.F.: A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157(1), 105\u2013132 (1982). http:\/\/www.sciencedirect.com\/science\/article\/pii\/0022283682905150","journal-title":"J. Mol. Biol."},{"key":"4_CR21","unstructured":"Labute, P., Santavy, M.: Locating binding sites in protein structures (2001). http:\/\/www.chemcomp.com\/journal\/sitefind.htm. Accessed 16 April 2015"},{"issue":"9","key":"4_CR22","doi-asserted-by":"publisher","first-page":"1908","DOI":"10.1093\/bioinformatics\/bti315","volume":"21","author":"A Laurie","year":"2005","unstructured":"Laurie, A., Jackson, R.: Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics (Oxford, England) 21(9), 1908\u20131916 (2005)","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"5","key":"4_CR23","doi-asserted-by":"publisher","first-page":"395","DOI":"10.2174\/138920306778559386","volume":"7","author":"A Laurie","year":"2006","unstructured":"Laurie, A., Jackson, R.: Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr. Protein Pept. Sci. 7(5), 395\u2013406 (2006)","journal-title":"Curr. Protein Pept. Sci."},{"issue":"1","key":"4_CR24","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/1471-2105-10-168","volume":"10","author":"V Le Guilloux","year":"2009","unstructured":"Le Guilloux, V., Schmidtke, P., Tuffery, P.: Fpocket: an open source platform for ligand pocket detection. BMC Bioinform. 10(1), 168 (2009). http:\/\/www.biomedcentral.com\/1471-2105\/10\/168","journal-title":"BMC Bioinform."},{"issue":"15","key":"4_CR25","doi-asserted-by":"publisher","first-page":"1550","DOI":"10.2174\/092986710790979944","volume":"17","author":"S Leis","year":"2010","unstructured":"Leis, S., Schneider, S., Zacharias, M.: In silico prediction of binding sites on proteins. Curr. Med. Chem. 17(15), 1550\u20131562 (2010)","journal-title":"Curr. Med. Chem."},{"issue":"4","key":"4_CR26","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/0263-7855(92)80074-N","volume":"10","author":"DG Levitt","year":"1992","unstructured":"Levitt, D.G., Banaszak, L.J.: Pocket: a computer graphies method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph. 10(4), 229\u2013234 (1992). http:\/\/www.sciencedirect.com\/science\/article\/pii\/026378559280074N","journal-title":"J. Mol. Graph."},{"issue":"2","key":"4_CR27","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1002\/prot.22067","volume":"73","author":"M Morita","year":"2008","unstructured":"Morita, M., Nakamura, S., Shimizu, K.: Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. Proteins 73(2), 468\u2013479 (2008)","journal-title":"Proteins"},{"issue":"2","key":"4_CR28","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1007\/s10969-008-9055-6","volume":"10","author":"R Nair","year":"2009","unstructured":"Nair, R., Liu, J., Soong, T.T., Acton, T., Everett, J., Kouranov, A., Fiser, A., Godzik, A., Jaroszewski, L., Orengo, C., et al.: Structural genomics is the largest contributor of novel structural leverage. J. Struct. Funct. Genom. 10(2), 181\u2013191 (2009)","journal-title":"J. Struct. Funct. Genom."},{"issue":"4","key":"4_CR29","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1002\/prot.20897","volume":"63","author":"M Nayal","year":"2006","unstructured":"Nayal, M., Honig, B.: On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 63(4), 892\u2013906 (2006)","journal-title":"Proteins"},{"issue":"15\u201316","key":"4_CR30","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1016\/j.drudis.2010.05.015","volume":"15","author":"S P\u00e9rot","year":"2010","unstructured":"P\u00e9rot, S., Sperandio, O., Miteva, M., Camproux, A., Villoutreix, B.: Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discovery Today 15(15\u201316), 656\u2013667 (2010)","journal-title":"Drug Discovery Today"},{"issue":"7","key":"4_CR31","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1093\/bioinformatics\/18.7.980","volume":"18","author":"A Pintar","year":"2002","unstructured":"Pintar, A., Carugo, O., Pongor, S.: Cx, an algorithm that identifies protruding atoms in proteins. Bioinformatics 18(7), 980\u2013984 (2002)","journal-title":"Bioinformatics"},{"key":"4_CR32","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.jtbi.2012.10.028","volume":"317","author":"Z Qiu","year":"2013","unstructured":"Qiu, Z., Qin, C., Jiu, M., Wang, X.: A simple iterative method to optimize protein-ligand-binding residue prediction. J. Theor. Biol. 317, 219\u2013223 (2013)","journal-title":"J. Theor. Biol."},{"issue":"12","key":"4_CR33","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.2174\/092986611797642788","volume":"18","author":"Z Qiu","year":"2011","unstructured":"Qiu, Z., Wang, X.: Improved prediction of protein ligand-binding sites using random forests. Protein Pept. Lett. 18(12), 1212\u20131218 (2011). http:\/\/www.ingentaconnect.com\/content\/ben\/ppl\/2011\/00000018\/00000012\/art00005","journal-title":"Protein Pept. Lett."},{"key":"4_CR34","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1002\/9783527633326.ch6","volume-title":"Docking Methods for Virtual Screening: Principles and Recent Advances","author":"D Rognan","year":"2011","unstructured":"Rognan, D.: Docking Methods for Virtual Screening: Principles and Recent Advances, pp. 153\u2013176. Wiley, Weinheim (2011). http:\/\/dx.doi.org\/10.1002\/9783527633326.ch6"},{"issue":"12","key":"4_CR35","doi-asserted-by":"publisher","first-page":"2191","DOI":"10.1021\/ci1000289","volume":"50","author":"P Schmidtke","year":"2010","unstructured":"Schmidtke, P., Souaille, C., Estienne, F., Baurin, N., Kroemer, R.: Large-scale comparison of four binding site detection algorithms. J. Chem. Inf. Model. 50(12), 2191\u20132200 (2010)","journal-title":"J. Chem. Inf. Model."},{"issue":"3","key":"4_CR36","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1016\/j.jsb.2012.09.010","volume":"180","author":"S Schneider","year":"2012","unstructured":"Schneider, S., Zacharias, M.: Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins. J. Struct. Biol. 180(3), 546\u2013550 (2012)","journal-title":"J. Struct. Biol."},{"issue":"6","key":"4_CR37","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1021\/ci500130e","volume":"54","author":"K Schomburg","year":"2014","unstructured":"Schomburg, K., Bietz, S., Briem, H., Henzler, A., Urbaczek, S., Rarey, M.: Facing the challenges of structure-based target prediction by inverse virtual screening. J. Chem. Inf. Model. 54(6), 1676\u20131686 (2014)","journal-title":"J. Chem. Inf. Model."},{"issue":"4","key":"4_CR38","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1093\/bib\/bbp017","volume":"10","author":"J Skolnick","year":"2009","unstructured":"Skolnick, J., Brylinski, M.: FINDSITE: a combined evolution\/structure-based approach to protein function prediction. Briefings Bioinform. 10(4), 378\u2013391 (2009)","journal-title":"Briefings Bioinform."},{"issue":"2","key":"4_CR39","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1021\/ci025584y","volume":"43","author":"C Steinbeck","year":"2003","unstructured":"Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E.: The chemistry development kit (CDK): an open-source java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43(2), 493\u2013500 (2003). pMID: 12653513","journal-title":"J. Chem. Inf. Comput. Sci."},{"issue":"6","key":"4_CR40","doi-asserted-by":"publisher","first-page":"1947","DOI":"10.1021\/ci034160g","volume":"43","author":"V Svetnik","year":"2003","unstructured":"Svetnik, V., Liaw, A., Tong, C., Culberson, J.C., Sheridan, R.P., Feuston, B.P.: Random forest: a classification and regression tool for compound classification and qsar modeling. J. chem. Inf. Comput. Sci. 43(6), 1947\u20131958 (2003)","journal-title":"J. chem. Inf. Comput. Sci."},{"issue":"1","key":"4_CR41","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1752-153X-1-7","volume":"1","author":"M Weisel","year":"2007","unstructured":"Weisel, M., Proschak, E., Schneider, G.: Pocketpicker: analysis of ligand binding-sites with shape descriptors. Chem. Central J. 1(1), 7 (2007). http:\/\/journal.chemistrycentral.com\/content\/1\/1\/7","journal-title":"Chem. Central J."},{"issue":"2","key":"4_CR42","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/j.sbi.2011.01.004","volume":"21","author":"L Xie","year":"2011","unstructured":"Xie, L., Xie, L., Bourne, P.E.: Structure-based systems biology for analyzing off-target binding. Curr. Opin. Struct. Biol. 21(2), 189\u2013199 (2011)","journal-title":"Curr. Opin. Struct. Biol."},{"issue":"15","key":"4_CR43","doi-asserted-by":"publisher","first-page":"2083","DOI":"10.1093\/bioinformatics\/btr331","volume":"27","author":"Z Zhang","year":"2011","unstructured":"Zhang, Z., Li, Y., Lin, B., Schroeder, M., Huang, B.: Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics (Oxford, England) 27(15), 2083\u20132088 (2011)","journal-title":"Bioinformatics (Oxford, England)"},{"key":"4_CR44","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1208\/s12248-012-9426-6","volume":"15","author":"X Zheng","year":"2012","unstructured":"Zheng, X., Gan, L., Wang, E., Wang, J.: Pocket-based drug design: exploring pocket space. AAPS J. 15, 228\u2013241 (2012)","journal-title":"AAPS J."}],"container-title":["Lecture Notes in Computer Science","Algorithms for Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-21233-3_4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,10]],"date-time":"2024-06-10T06:29:28Z","timestamp":1718000968000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-21233-3_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319212326","9783319212333"],"references-count":44,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-21233-3_4","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015]]},"assertion":[{"value":"28 July 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}