{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T07:38:35Z","timestamp":1740123515040,"version":"3.37.3"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2015,9,19]],"date-time":"2015-09-19T00:00:00Z","timestamp":1442620800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council (GB)","doi-asserted-by":"publisher","award":["EP\/G037280\/1"],"award-info":[{"award-number":["EP\/G037280\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2015,10]]},"DOI":"10.1007\/s10822-015-9866-z","type":"journal-article","created":{"date-parts":[[2015,9,19]],"date-time":"2015-09-19T04:10:12Z","timestamp":1442635812000},"page":"963-973","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["WONKA: objective novel complex analysis for ensembles of protein\u2013ligand structures"],"prefix":"10.1007","volume":"29","author":[{"given":"A. R.","family":"Bradley","sequence":"first","affiliation":[]},{"given":"I. D.","family":"Wall","sequence":"additional","affiliation":[]},{"given":"F.","family":"von Delft","sequence":"additional","affiliation":[]},{"given":"D. V. S.","family":"Green","sequence":"additional","affiliation":[]},{"given":"C. M.","family":"Deane","sequence":"additional","affiliation":[]},{"given":"B. D.","family":"Marsden","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,9,19]]},"reference":[{"key":"9866_CR1","unstructured":"Murray CW, Rees DC (2009) The rise of fragment-based drug discovery. Nat Chem, Astex Therapeutics, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK. 1:187\u2013192"},{"key":"9866_CR2","doi-asserted-by":"crossref","unstructured":"Feyfant E, Cross JB, Paris K, Tsao DH (2011) Fragment-based drug design. Methods Mol Biol, Pfizer Global R&D, Cambridge, MA, USA. 685:241\u2013252","DOI":"10.1007\/978-1-60761-931-4_12"},{"key":"9866_CR3","doi-asserted-by":"crossref","first-page":"12857","DOI":"10.3390\/ijms131012857","volume":"13","author":"Z Chilingaryan","year":"2012","unstructured":"Chilingaryan Z, Yin Z, Oakley AJ (2012) Fragment-based screening by protein crystallography: successes and pitfalls. Int J Mol Sci 13:12857\u201312879","journal-title":"Int J Mol Sci"},{"key":"9866_CR4","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1186\/1471-2105-15-324","volume":"15","author":"WR Pitt","year":"2014","unstructured":"Pitt WR, Montalv\u00e3o RW, Blundell TL (2014) Polyphony: superposition independent methods for ensemble-based drug discovery. BMC Bioinform 15:324","journal-title":"BMC Bioinform"},{"key":"9866_CR5","unstructured":"Schr\u00f6dinger LLC (2010) The {PyMOL} molecular graphics system, version ~1.3r1"},{"key":"9866_CR6","doi-asserted-by":"crossref","first-page":"R121","DOI":"10.1186\/gb-2008-9-8-r121","volume":"9","author":"E Hodis","year":"2008","unstructured":"Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL (2008) Proteopedia-a scientific \u201cwiki\u201d bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol 9:R121","journal-title":"Genome Biol"},{"key":"9866_CR7","doi-asserted-by":"crossref","unstructured":"Cross S, Baroni M, Goracci L, Cruciani G (2012) GRID-based three-dimensional pharmacophores I: FLAPpharm, a novel approach for pharmacophore elucidation. J Chem Inf Model, American Chemical Society 52:2587\u201398","DOI":"10.1021\/ci300153d"},{"key":"9866_CR8","doi-asserted-by":"crossref","unstructured":"Salam NK, Nuti R, Sherman W (2009) Novel method for generating structure-based pharmacophores using energetic analysis. J Chem Inf Model, American Chemical Society 49:2356\u201368","DOI":"10.1021\/ci900212v"},{"key":"9866_CR9","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.2174\/092986708784049630","volume":"15","author":"H Sun","year":"2008","unstructured":"Sun H (2008) Pharmacophore-based virtual screening. Curr Med Chem 15:1018\u20131024","journal-title":"Curr Med Chem"},{"key":"9866_CR10","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/978-1-60761-839-3_11","volume":"672","author":"D Horvath","year":"2011","unstructured":"Horvath D (2011) Pharmacophore-based virtual screening. Methods Mol Biol 672:261\u2013298","journal-title":"Methods Mol Biol"},{"key":"9866_CR11","unstructured":"Seeliger D, de Groot BL (2010) Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Gottingen, Germany. 6:e1000634"},{"key":"9866_CR12","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1002\/(SICI)1097-0134(199703)27:3<425::AID-PROT10>3.0.CO;2-N","volume":"27","author":"S Hayward","year":"1997","unstructured":"Hayward S, Kitao A, Berendsen HJ (1997) Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27:425\u2013437","journal-title":"Proteins"},{"key":"9866_CR13","doi-asserted-by":"crossref","unstructured":"Allain A, Chauvot de Beauch\u00eane I, Langenfeld F, Guarracino Y, Laine E, Tchertanov L (2014) Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs. Faraday Discuss. The Royal Society of Chemistry 169:303\u201321","DOI":"10.1039\/C4FD00024B"},{"key":"9866_CR14","doi-asserted-by":"crossref","unstructured":"Ross GA, Morris GM, Biggin PC (2012) Rapid and accurate prediction and scoring of water molecules in protein binding sites. PLoS One (Csermely, P., Ed.), Public Library of Science 7:e32036","DOI":"10.1371\/journal.pone.0032036"},{"key":"9866_CR15","doi-asserted-by":"crossref","unstructured":"Bodnarchuk MS, Viner R, Michel J, Essex JW (2014) Strategies to calculate water binding free energies in protein-ligand complexes. J Chem Inf Model, American Chemical Society 54:1623\u201333","DOI":"10.1021\/ci400674k"},{"key":"9866_CR16","doi-asserted-by":"crossref","first-page":"2978","DOI":"10.1093\/bioinformatics\/btu424","volume":"30","author":"H Patel","year":"2014","unstructured":"Patel H, Gr\u00fcning BA, G\u00fcnther S, Merfort I (2014) PyWATER: a PyMOL plug-into find conserved water molecules in proteins by clustering. Bioinformatics 30:2978\u20132980","journal-title":"Bioinformatics"},{"key":"9866_CR17","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1002\/jcc.540150503","volume":"15","author":"R Abagyan","year":"1994","unstructured":"Abagyan R, Totrov M, Kuznetsov D (1994) ICM?A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488\u2013506","journal-title":"J Comput Chem"},{"key":"9866_CR18","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","volume":"112","author":"FC Bernstein","year":"1977","unstructured":"Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535\u2013542","journal-title":"J Mol Biol"},{"key":"9866_CR19","unstructured":"Landrum G, RDKit: open-source cheminformatics. http:\/\/www.rdkit.org"},{"key":"9866_CR20","unstructured":"Foundation PS, Python language reference, version 2.7.3. https:\/\/www.python.org\/"},{"key":"9866_CR21","unstructured":"Django Software Foundation (2013) Django (version 1.5). https:\/\/www.djangoproject.com\/"},{"key":"9866_CR22","unstructured":"SMARTS Inc. Daylight chemical information systems Santa Fe, NM, vol 471. http:\/\/www.daylight.com\/dayhtml\/doc\/theory\/theory.smarts.html"},{"key":"9866_CR23","doi-asserted-by":"crossref","unstructured":"Wilcken R, Zimmermann MO, Lange A, Joerger AC, Boeckler FM (2013) Principles and applications of halogen bonding in medicinal chemistry and chemical biology. J Med Chem, American Chemical Society 56:1363\u201388","DOI":"10.1021\/jm3012068"},{"key":"9866_CR24","doi-asserted-by":"crossref","first-page":"12256","DOI":"10.1002\/anie.201303207","volume":"52","author":"H Sch\u00f6nherr","year":"2013","unstructured":"Sch\u00f6nherr H, Cernak T (2013) Profound methyl effects in drug discovery and a call for new C-H methylation reactions. Angew Chem Int Ed Engl 52:12256\u201312267","journal-title":"Angew Chem Int Ed Engl"},{"key":"9866_CR25","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1021\/ci900450m","volume":"50","author":"J Hussain","year":"2010","unstructured":"Hussain J, Rea C (2010) Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets. J Chem Inf Model 50:339\u2013348","journal-title":"J Chem Inf Model"},{"key":"9866_CR26","doi-asserted-by":"crossref","first-page":"2636","DOI":"10.1021\/ci500245d","volume":"54","author":"AR Bradley","year":"2014","unstructured":"Bradley AR, Wall ID, Green DVS, Deane CM, Marsden BD (2014) OOMMPPAA: a tool to aid directed synthesis by the combined analysis of activity and structural data. J Chem Inf Model 54:2636\u20132646","journal-title":"J Chem Inf Model"},{"key":"9866_CR27","unstructured":"Kulis B, Jordan MI (2011) Revisiting k-means: new algorithms via Bayesian nonparametrics. http:\/\/arxiv.org\/abs\/1111.0352"},{"key":"9866_CR28","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1021\/ci100050t","volume":"50","author":"D Rogers","year":"2010","unstructured":"Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50:742\u2013754","journal-title":"J Chem Inf Model"},{"key":"9866_CR29","doi-asserted-by":"crossref","unstructured":"Butina D (1999) Unsupervised data base clustering based on daylight\u2019s fingerprint and tanimoto similarity: a fast and automated way to cluster small and large data sets. J Chem Inf Model, American Chemical Society 39:747\u2013750","DOI":"10.1021\/ci9803381"},{"key":"9866_CR30","doi-asserted-by":"crossref","unstructured":"Raush E, Totrov M, Marsden BD, Abagyan R (2009) A new method for publishing three-dimensional content. PLoS One (Gay, N., Ed.), Public Library of Science. 4:e7394","DOI":"10.1371\/journal.pone.0007394"},{"key":"9866_CR31","doi-asserted-by":"crossref","first-page":"e7675","DOI":"10.1371\/journal.pone.0007675","volume":"4","author":"WH Lee","year":"2009","unstructured":"Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD (2009) SGC\u2013structural biology and human health: a new approach to publishing structural biology results. PLoS One 4:e7675","journal-title":"PLoS One"},{"key":"9866_CR32","doi-asserted-by":"crossref","first-page":"2205","DOI":"10.1093\/bioinformatics\/bts340","volume":"28","author":"L Liu","year":"2012","unstructured":"Liu L, Zhen XT, Denton E, Marsden BD, Schapira M (2012) ChromoHub: a data hub for navigators of chromatin-mediated signalling. Bioinformatics 28:2205\u20132206","journal-title":"Bioinformatics"},{"key":"9866_CR33","unstructured":"Disqus\u2014The web\u2019s community of communities. https:\/\/disqus.com\/"},{"key":"9866_CR34","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1016\/j.str.2009.02.010","volume":"17","author":"DL Mobley","year":"2009","unstructured":"Mobley DL, Dill KA (2009) Binding of small-molecule ligands to proteins: \u201cwhat you see\u201d is not always \u201cwhat you get\u201d. Structure\u00a017:489\u2013498","journal-title":"Structure"},{"key":"9866_CR35","doi-asserted-by":"crossref","unstructured":"Abel R, Young T, Farid R, Berne BJ, Friesner RA (2008) Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc, American Chemical Society 130:2817\u201331","DOI":"10.1021\/ja0771033"},{"key":"9866_CR36","unstructured":"Filippakopoulos P, Knapp S (2014) Targeting bromodomains: epigenetic readers of lysine acetylation. Nat Rev Drug Discov, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 13:337\u201356"},{"key":"9866_CR37","unstructured":"Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert J-P, Barsyte-Lovejoy D, Felletar I, Volkmer R, M\u00fcller S, Pawson T, Gingras A-C, Arrowsmith CH, Knapp S (2012) Histone recognition and large-scale structural analysis of the human bromodomain family. Cell. Elsevier Inc, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK. 149:214\u201331"},{"key":"9866_CR38","doi-asserted-by":"crossref","unstructured":"Ferguson FM, Dias DM, Rodrigues JPGLM, Wienk H, Boelens R, Bonvin AMJJ, Abell C, Ciulli A (2014) Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking. Biochemistry, American Chemical Society 53:6706","DOI":"10.1021\/bi500909d"},{"key":"9866_CR39","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1002\/cmdc.201300156","volume":"9","author":"D Huang","year":"2014","unstructured":"Huang D, Rossini E, Steiner S, Caflisch A (2014) Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem 9:573\u2013579","journal-title":"ChemMedChem"},{"key":"9866_CR40","doi-asserted-by":"crossref","unstructured":"Hewings DS, Rooney TPC, Jennings LE, Hay DA, Schofield CJ, Brennan PE, Knapp S, Conway SJ (2012) Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. J Med Chem, American Chemical Society 55:9393\u2013413","DOI":"10.1021\/jm300915b"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-015-9866-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-015-9866-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-015-9866-z","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,3,26]],"date-time":"2019-03-26T15:05:42Z","timestamp":1553612742000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-015-9866-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,9,19]]},"references-count":40,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2015,10]]}},"alternative-id":["9866"],"URL":"https:\/\/doi.org\/10.1007\/s10822-015-9866-z","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2015,9,19]]}}}