{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T05:06:33Z","timestamp":1768885593207,"version":"3.49.0"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2015,12,9]],"date-time":"2015-12-09T00:00:00Z","timestamp":1449619200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004630","type":"journal-article","created":{"date-parts":[[2015,12,10]],"date-time":"2015-12-10T01:19:59Z","timestamp":1449710399000},"page":"e1004630","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["Text Mining for Protein Docking"],"prefix":"10.1371","volume":"11","author":[{"given":"Varsha D.","family":"Badal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petras J.","family":"Kundrotas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilya A.","family":"Vakser","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,12,9]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/S0959-440X(97)80027-9","article-title":"Advances in comparative protein-structure modeling","volume":"7","author":"R Sanchez","year":"1997","journal-title":"Curr Opin Struct Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1016\/j.jmb.2003.07.006","article-title":"The relationship between sequence and interaction divergence in proteins","volume":"332","author":"P Aloy","year":"2003","journal-title":"J Mol Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1002\/prot.10222","article-title":"MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading","volume":"49","author":"L Lu","year":"2002","journal-title":"Proteins"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"9438","DOI":"10.1073\/pnas.1200678109","article-title":"Templates are available to model nearly all complexes of structurally characterized proteins","volume":"109","author":"PJ Kundrotas","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: A protein-protein docking approach based on biochemical or biophysical information","volume":"125","author":"C Dominguez","year":"2003","journal-title":"J Am Chem Soc"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1016\/j.bpj.2014.08.033","article-title":"Protein-protein docking: From interaction to interactome","volume":"107","author":"IA Vakser","year":"2014","journal-title":"Biophys J"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1016\/j.sbi.2013.06.017","article-title":"Scoring functions for protein\u2013protein interactions","volume":"23","author":"IH Moal","year":"2013","journal-title":"Curr Opin Struct Biol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1002\/prot.24428","article-title":"Docking, scoring, and affinity prediction in CAPRI","volume":"81","author":"MF Lensink","year":"2013","journal-title":"Proteins"},{"key":"ref10","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baq026","article-title":"Literature curation of protein interactions: Measuring agreement across major public databases","volume":"2010","author":"AL Turinsky","year":"2010","journal-title":"Database"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/gb-2005-6-7-224","article-title":"Text-mining and information-retrieval services for molecular biology","volume":"6","author":"M Krallinger","year":"2005","journal-title":"Genome Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/nrg3337","article-title":"Text-mining solutions for biomedical research: Enabling integrative biology","volume":"13","author":"D Rebholz-Schuhmann","year":"2012","journal-title":"Nature Rev Genetics"},{"key":"ref13","unstructured":"Seoud AA, Solouma NH, Youssef AM, Kadah YM, editors. Extraction of protein interaction information from unstructured text using a link grammar parser. ICCES &apos;07 International Conference on Computer Engineering &amp; Systems 2007; 2007."},{"key":"ref14","doi-asserted-by":"crossref","first-page":"2046","DOI":"10.1093\/bioinformatics\/btg279","article-title":"Extraction of protein interaction information from unstructured text using a context-free grammar","volume":"19","author":"JMG Temkin","year":"2003","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.1016\/j.ijmedinf.2009.04.010","article-title":"Protein\u2013protein interaction extraction by leveraging multiple kernels and parsers","volume":"78","author":"M Miwa","year":"2009","journal-title":"Int J Med Inform"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/S1359-6446(05)03376-3","article-title":"Text-mining approaches in molecular biology and biomedicine","volume":"10","author":"M Krallinger","year":"2005","journal-title":"Drug Discov Today"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/bioinformatics\/btp602","article-title":"Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D","volume":"26","author":"Y Niu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1093\/bioinformatics\/bts042","article-title":"Literature mining of host\u2013pathogen interactions: Comparing feature-based supervised learning and language-based approaches","volume":"28","author":"T Thieu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2105-4-11","article-title":"PreBIND and Textomy\u2013mining the biomedical literature for protein-protein interactions using a support vector machine","volume":"4","author":"I Donaldson","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"D396","DOI":"10.1093\/nar\/gkt1079","article-title":"Negatome 2.0: A database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis","volume":"42","author":"P Blohm","year":"2014","journal-title":"Nucl Acid Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/1471-2105-13-172","article-title":"A text-mining system for extracting metabolic reactions from full-text articles","volume":"13","author":"J Czarnecki","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2164-13-S4-S10","article-title":"Automated extraction and semantic analysis of mutation impacts from the biomedical literature","volume":"13","author":"N Naderi","year":"2012","journal-title":"BMC Genom"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.ymeth.2014.10.027","article-title":"Text as data: Using text-based features for proteins representation and for computational prediction of their characteristics","volume":"74","author":"H Shatkay","year":"2015","journal-title":"Methods"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e32171","DOI":"10.1371\/journal.pone.0032171","article-title":"Text mining improves prediction of protein functional sites","volume":"7","author":"KM Verspoor","year":"2012","journal-title":"PloS One"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.ymeth.2014.10.026","article-title":"Protein-protein interaction predictions using text mining methods","volume":"74","author":"N Papanikolaou","year":"2014","journal-title":"Methods"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"i180","DOI":"10.1093\/bioinformatics\/btg1023","article-title":"GENIA corpus\u2014a semantically annotated corpus for bio-textmining","volume":"19","author":"JD Kim","year":"2003","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1186\/1471-2105-12-435","article-title":"PESCADOR, a web-based tool to assist textmining of biointeractions extracted from PubMed queries","volume":"12","author":"A Barbosa-Silva","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/1471-2105-11-70","article-title":"LAITOR\u2014Literature Assistant for Identification of Terms co-Occurrences and Relationships","volume":"11","author":"A Barbosa-Silva","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e33427","DOI":"10.1371\/journal.pone.0033427","article-title":"Text mining for literature review and knowledge discovery in cancer risk assessment and research","volume":"7","author":"A Korhonen","year":"2012","journal-title":"PloS One"},{"issue":"Suppl 8","key":"ref30","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1186\/1471-2105-12-S8-S9","article-title":"Classifying protein-protein interaction articles using word and syntactic features","volume":"12","author":"S Kim","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1093\/bioinformatics\/btr702","article-title":"PIE the search: Searching PubMed literature for protein interaction information","volume":"28","author":"S Kim","year":"2012","journal-title":"Bioinformatics"},{"key":"ref32","article-title":"The eFIP system for text mining of protein interaction networks of phosphorylated proteins","author":"CO Tudor","year":"2012","journal-title":"Database"},{"key":"ref33","article-title":"PPInterFinder\u2014a mining tool for extracting causal relations on human proteins from literature","author":"K Raja","year":"2013","journal-title":"Database"},{"key":"ref34","article-title":"Assisting manual literature curation for protein-protein interactions using BioQRator","author":"D Kwon","year":"2014","journal-title":"Database"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"D191","DOI":"10.1093\/nar\/gkt1140","article-title":"Activities at the Universal Protein Resource (UniProt)","volume":"42","author":"U Consortium","year":"2014","journal-title":"Nucl Acid Res"},{"key":"ref36","first-page":"475","article-title":"Mapping in PubMed","volume":"90","author":"LWS Knecht","year":"2002","journal-title":"J Med Lib Assoc"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1126\/science.4023714","article-title":"Hydrophobicity of amino acid residues in globular proteins","volume":"229","author":"GD Rose","year":"1985","journal-title":"Science"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1002\/prot.340110407","article-title":"Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons","volume":"11","author":"A Nicholls","year":"1991","journal-title":"Proteins"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"4297","DOI":"10.1093\/bioinformatics\/bti694","article-title":"Mapping PDB chains to UniProtKB entries","volume":"21","author":"ACR Martin","year":"2005","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s10791-007-9027-7","article-title":"An empirical study of tokenization strategies for biomedical information retrieval","volume":"10","author":"J Jiang","year":"2007","journal-title":"Inform Retrieval"},{"key":"ref41","first-page":"130","article-title":"An algorithm for suffix stripping","volume":"14","author":"MF Porter","year":"1980","journal-title":"Program-Electon Lib"},{"key":"ref42","first-page":"169","author":"T Joachims","year":"1999"},{"key":"ref43","unstructured":"Morik K, Brockhausen P, Joachims T. Combining statistical learning with a knowledge-based approach: A case study in intensive care monitoring. Technical Report, SFB 475: Komplexitatsreduktion in Multivariaten Datenstrukturen (No. 1999, 24). Universitat Dortmund1999."},{"key":"ref44","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1089\/106652703322756104","article-title":"Mining the biomedical literature in the genomic era: An overview","volume":"10","author":"H Shatkay","year":"2003","journal-title":"J Comp Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1021\/ci0341161","article-title":"Comparison of support vector machine and artificial neural network systems for drug\/nondrug classification","volume":"43","author":"E Byvatov","year":"2003","journal-title":"J Chem Inf Comput Sci"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1002\/prot.21714","article-title":"DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking","volume":"69","author":"Y Gao","year":"2007","journal-title":"Proteins"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/protein\/8.4.371","article-title":"Protein docking for low-resolution structures","volume":"8","author":"IA Vakser","year":"1995","journal-title":"Protein Eng"},{"key":"ref48","first-page":"137","article-title":"Machine Learning: ECML-98","author":"T Joachims","year":"1998"},{"key":"ref49","first-page":"606","article-title":"Computer and Information Sciences-ISCIS 2005","author":"A Ozgur","year":"2005"},{"key":"ref50","first-page":"1441","article-title":"Poetry classification using support vector machines","volume":"8","author":"N Jamal","year":"2012"},{"issue":"Suppl 3","key":"ref51","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1471-2105-14-S3-S14","article-title":"Protein function prediction using text-based features extracted from the biomedical literature: The CAFA challenge","volume":"14","author":"A Wong","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/j.neuroscience.2007.04.047","article-title":"Intracerebroventricular administration of an endothelin ETB receptor agonist increases expression of tissue inhibitor of matrix metalloproteinase-1 and -3 in rat brain","volume":"147","author":"Y Koyama","year":"2007","journal-title":"Neuroscience"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2634","DOI":"10.1093\/bioinformatics\/btn497","article-title":"DOCKGROUND protein-protein docking decoy set","volume":"24","author":"S Liu","year":"2008","journal-title":"Bioinformatics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004630","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T09:09:24Z","timestamp":1567415364000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004630"}},"subtitle":[],"editor":[{"given":"Nir","family":"Ben-Tal","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,12,9]]},"references-count":53,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2015,12,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004630","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12,9]]}}}