{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T14:57:36Z","timestamp":1760367456448},"reference-count":53,"publisher":"American Chemical Society (ACS)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2008,11,24]]},"DOI":"10.1021\/ci800200e","type":"journal-article","created":{"date-parts":[[2008,10,21]],"date-time":"2008-10-21T10:00:44Z","timestamp":1224583244000},"page":"2278-2288","source":"Crossref","is-referenced-by-count":30,"title":["Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space"],"prefix":"10.1021","volume":"48","author":[{"given":"Helena","family":"Str\u00f6mbergsson","sequence":"first","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]},{"given":"Pawel","family":"Daniluk","sequence":"additional","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]},{"given":"Andriy","family":"Kryshtafovych","sequence":"additional","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]},{"given":"Krzysztof","family":"Fidelis","sequence":"additional","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]},{"given":"Jarl E. S.","family":"Wikberg","sequence":"additional","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]},{"given":"Gerard J.","family":"Kleywegt","sequence":"additional","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]},{"given":"Torgeir R.","family":"Hvidsten","sequence":"additional","affiliation":[{"name":"The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden, Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland, Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, Warsaw, Poland, UC Davis Genome Centre, UC Davis, Davis, California, Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, and Ume\u00e5 Plant Science..."}]}],"member":"316","published-online":{"date-parts":[[2008,10,21]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/S1056-8719(00)00107-6","volume":"44","author":"Lipinski C. A.","year":"2000","journal-title":"J. Pharmacol. Toxicol. Methods"},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/sj.bjp.0707307","volume":"152","author":"Rognan D.","year":"2007","journal-title":"Br. J. Pharmacol."},{"key":"ref3\/cit3","doi-asserted-by":"crossref","first-page":"213","DOI":"10.2174\/138620706776055539","volume":"9","author":"Dudek A. Z.","year":"2006","journal-title":"Comb. Chem. High Throughput Screening"},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1016\/j.cbpa.2007.08.033","volume":"11","author":"McInnes C.","year":"2007","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref5\/cit5","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1093\/protein\/15.4.305","volume":"4","author":"Prusis P.","year":"2002","journal-title":"Protein Eng."},{"key":"ref6\/cit6","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1023\/A:1020155510718","volume":"16","author":"Taylor R. D.","year":"2002","journal-title":"J. Comput.-Aided. Mol. Des."},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"5912","DOI":"10.1021\/jm050362n","volume":"49","author":"Warren G. L.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/1471-2105-9-184","volume":"9","author":"Sauton N.","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref9\/cit9","first-page":"1","volume-title":"Chemoinformatics: a textbook","author":"Gasteiger J.","year":"2003"},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1002\/3527601643.ch8","volume-title":"Chemoinformatics","author":"Terfloth L.","year":"2003"},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1016\/j.drudis.2007.08.004","volume":"12","author":"Lill M. A.","year":"2007","journal-title":"Drug Discovery Today"},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/S0304-4165(00)00187-2","volume":"1525","author":"Lapinsh M.","year":"2001","journal-title":"Biochim. Biophys. Acta"},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/S0167-4838(00)00249-1","volume":"1544","author":"Prusis P.","year":"2001","journal-title":"Biochim. Biophys. Acta"},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1002\/prot.20777","volume":"63","author":"Str\u00f6mbergsson H.","year":"2006","journal-title":"Proteins"},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1021\/jm020945m","volume":"46","author":"Lapinsh M.","year":"2003","journal-title":"J. Med. Chem."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"4289","DOI":"10.1093\/bioinformatics\/bti703","volume":"21","author":"Lapinsh M.","year":"2005","journal-title":"Bioinformatics"},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"2481","DOI":"10.1021\/jm9700575","volume":"41","author":"Sandberg M.","year":"1998","journal-title":"J. Med. Chem."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1371\/journal.pcbi.0030048","volume":"3","author":"Kontijevskis A.","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1021\/ci050323k","volume":"46","author":"Lindstr\u00f6m A.","year":"2006","journal-title":"J. Chem. Inf. Model."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1002\/prot.21332","volume":"67","author":"Jain T.","year":"2007","journal-title":"Proteins"},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1021\/ci050006d","volume":"45","author":"Bock J. R.","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"II81\u2212II91","DOI":"10.1093\/bioinformatics\/btg047","volume":"19","author":"Hvidsten T. R.","year":"2003","journal-title":"Bioinformatics"},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1002\/prot.21163","volume":"65","author":"Str\u00f6mbergsson H.","year":"2006","journal-title":"Proteins"},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/nar\/28.1.304","volume":"28","author":"Bairoch A.","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(00)00129-0","volume":"46","author":"Lipinski C. A.","year":"2001","journal-title":"Adv. Drug Delivery Rev."},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"6716","DOI":"10.1021\/jm060167o","volume":"49","author":"Bostr\u00f6m J.","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"D522","DOI":"10.1093\/nar\/gkj039","volume":"34","author":"Block P.","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"4111","DOI":"10.1021\/jm048957q","volume":"48","author":"Wang R.","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1002\/prot.20512","volume":"60","author":"Hu L.","year":"2005","journal-title":"Proteins"},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"1856","DOI":"10.1093\/bioinformatics\/btg243","volume":"19","author":"Puvanendrampillai D.","year":"2003","journal-title":"Bioinformatics"},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"Berman H. M.","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkh078","volume":"32","author":"Golovin A.","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"D431","DOI":"10.1093\/nar\/gkh081","volume":"32","author":"Schomburg I.","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"D266","DOI":"10.1093\/nar\/gki001","volume":"33","author":"Laskowski R. A.","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1093\/bioinformatics\/bti749","volume":"22","author":"Liu H.","year":"2006","journal-title":"Bioinformatics"},{"key":"ref36\/cit36","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"Laskowski R. A.","year":"1993","journal-title":"J. Appl. Crystallogr."},{"key":"ref37\/cit37","unstructured":"ProCheck operating manual appendix E.http:\/\/www.biochem.ucl.ac.uk\/\u223croman\/procheck\/manual\/manappe.html(accessed March 3, 2008) ."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/0898-5529(90)90156-3","volume":"3","author":"Gasteiger J.","year":"1990","journal-title":"Tetrahedron Comp. Method."},{"key":"ref39\/cit39","unstructured":"Dragon-Software for the calculation of molecular descriptors, 2.1; Talete srl: Milan, Italy, 2002."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","unstructured":"Hvidsten, T. R.; Kryshtafovych, A.; Fidelis, K.Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions.Proteins2008, in press.","DOI":"10.1002\/prot.22296"},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/nar\/28.1.254","volume":"28","author":"Brenner S. E.","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"Needleman S. B.","year":"1970","journal-title":"J. Mol. Biol."},{"key":"ref43\/cit43","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"Rice P.","year":"2000","journal-title":"Trends Genet."},{"key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1021\/ci050400b","volume":"46","author":"Guha R.","year":"2006","journal-title":"J. Chem. Inf. Model."},{"key":"ref45\/cit45","unstructured":"The, R\u2009suite of statistics software.http:\/\/www.r-project.org\/(accessed April 7, 2008) ."},{"key":"ref46\/cit46","unstructured":"Johnson, R. A.; Wichern, D. W. Clustering, distance methods and ordination. InApplied multivariate statistical analysis;Prentice-Hall: Upper Saddle River, NJ, 1998; pp, 726\u2212799."},{"key":"ref47\/cit47","doi-asserted-by":"crossref","unstructured":"Chang, C.C.; Lin, C.J.LIBSVM: a library for support vector machines.http:\/\/www.csie.ntu.edu.tw\/\u223ccjlin\/libsvm(accessed Oct 1, 2007) .","DOI":"10.1145\/1961189.1961199"},{"key":"ref48\/cit48","doi-asserted-by":"crossref","unstructured":"Hastie, T. Tibshirani, R. Friedman, J. InThe elements of statistical learning.Springer-Verlag: New York, 2001; pp, 371\u2212376.","DOI":"10.1007\/978-0-387-21606-5_12"},{"key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"3426","DOI":"10.1021\/bi036152z","volume":"43","author":"Cona A.","year":"2004","journal-title":"Biochemistry"},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"21847","DOI":"10.1074\/jbc.M501100200","volume":"280","author":"Baldwin J.","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1021\/jm060687j","volume":"50","author":"Heikkila T.","year":"2007","journal-title":"J. Med. Chem."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"6291","DOI":"10.1021\/jm701143p","volume":"50","author":"Martin R. E.","year":"2007","journal-title":"J. Med. Chem."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"6295","DOI":"10.1021\/jm701144e","volume":"50","author":"Guba W.","year":"2007","journal-title":"J. Med. Chem."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/ci800200e","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T04:09:58Z","timestamp":1680581398000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/ci800200e"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,21]]},"references-count":53,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2008,11,24]]}},"alternative-id":["10.1021\/ci800200e"],"URL":"https:\/\/doi.org\/10.1021\/ci800200e","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,21]]}}}