{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T03:33:49Z","timestamp":1775100829645,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T00:00:00Z","timestamp":1578528000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2016-05369"],"award-info":[{"award-number":["2016-05369"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Swedish e-Science Research Center and the Foundation Blanceflor Boncompagni Ludovisi, n\u00e9e Bildt"},{"DOI":"10.13039\/501100015730","name":"National Supercomputer Centre","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100015730","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>InterPep2 is a freely available method for predicting the structure of peptide\u2013protein interactions. Improved performance is obtained by using templates from both peptide\u2013protein and regular protein\u2013protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide\u2013protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0\u2009\u00c5 LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide\u2013protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0\u2009\u00c5 LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The program is available from: http:\/\/wallnerlab.org\/InterPep2.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa005","type":"journal-article","created":{"date-parts":[[2020,1,3]],"date-time":"2020-01-03T20:20:00Z","timestamp":1578082800000},"page":"2458-2465","source":"Crossref","is-referenced-by-count":41,"title":["InterPep2: global peptide\u2013protein docking using interaction surface templates"],"prefix":"10.1093","volume":"36","author":[{"given":"Isak","family":"Johansson-\u00c5khe","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology , Link\u00f6ping University, Link\u00f6ping, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7868-034X","authenticated-orcid":false,"given":"Claudio","family":"Mirabello","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology , Link\u00f6ping University, Link\u00f6ping, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3772-8279","authenticated-orcid":false,"given":"Bj\u00f6rn","family":"Wallner","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology , Link\u00f6ping University, Link\u00f6ping, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2020,1,9]]},"reference":[{"key":"2023013110261057300_btaa005-B1","doi-asserted-by":"crossref","first-page":"e1005905","DOI":"10.1371\/journal.pcbi.1005905","article-title":"High-resolution global peptide\u2013protein docking using fragments-based PIPER-FlexPepDock","volume":"13","author":"Alam","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"2023013110261057300_btaa005-B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B3","doi-asserted-by":"crossref","first-page":"e55","DOI":"10.1158\/0008-5472.CAN-17-0511","article-title":"DINC 2.0: a new protein\u2013peptide docking webserver using an incremental approach","volume":"77","author":"Antunes","year":"2017","journal-title":"Cancer Res"},{"key":"2023013110261057300_btaa005-B4","doi-asserted-by":"crossref","first-page":"W344","DOI":"10.1093\/nar\/gkw408","article-title":"ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules","volume":"44","author":"Ashkenazy","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B5","doi-asserted-by":"crossref","first-page":"W285","DOI":"10.1093\/nar\/gku397","article-title":"Prism: a web server and repository for prediction of protein\u2013protein interactions and modeling their 3D complexes","volume":"42","author":"Baspinar","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B6","doi-asserted-by":"crossref","first-page":"e0161879","DOI":"10.1371\/journal.pone.0161879","article-title":"DockQ: a quality measure for protein\u2013protein docking models","volume":"11","author":"Basu","year":"2016","journal-title":"PLoS One"},{"key":"2023013110261057300_btaa005-B7","doi-asserted-by":"crossref","first-page":"i262","DOI":"10.1093\/bioinformatics\/btw257","article-title":"Finding correct protein\u2013protein docking models using proQDock","volume":"32","author":"Basu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013110261057300_btaa005-B8","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1002\/pro.5560061021","article-title":"Protein\u2013protein crystal-packing contacts","volume":"6","author":"Carugo","year":"2008","journal-title":"Protein Sci"},{"key":"2023013110261057300_btaa005-B9","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1529\/biophysj.107.114280","article-title":"M-TASSER: an algorithm for protein quaternary structure prediction","volume":"94","author":"Chen","year":"2008","journal-title":"Biophys. J"},{"key":"2023013110261057300_btaa005-B10","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein\u2013protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. Am. Chem. Soc"},{"key":"2023013110261057300_btaa005-B11","doi-asserted-by":"crossref","first-page":"e23294","DOI":"10.1371\/journal.pone.0023294","article-title":"Generalized fragment picking in ROSETTA: design, protocols and applications","volume":"6","author":"Gront","year":"2011","journal-title":"PLoS One"},{"key":"2023013110261057300_btaa005-B12","doi-asserted-by":"crossref","first-page":"4267","DOI":"10.1038\/s41598-019-38498-7","article-title":"Predicting protein\u2013peptide interaction sites using distant protein complexes as structural templates","volume":"9","author":"Johansson-\u00c5khe","year":"2019","journal-title":"Sci. Rep"},{"key":"2023013110261057300_btaa005-B13","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"Jones","year":"1999","journal-title":"J. Mol. Biol"},{"key":"2023013110261057300_btaa005-B14","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1002\/prot.21117","article-title":"PIPER: an FFT-based protein docking program with pairwise potentials","volume":"65","author":"Kozakov","year":"2006","journal-title":"Proteins"},{"key":"2023013110261057300_btaa005-B15","doi-asserted-by":"crossref","first-page":"10383","DOI":"10.1073\/pnas.97.19.10383","article-title":"Native protein sequences are close to optimal for their structures","volume":"97","author":"Kuhlman","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013110261057300_btaa005-B16","doi-asserted-by":"crossref","first-page":"W419","DOI":"10.1093\/nar\/gkv456","article-title":"CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site","volume":"43","author":"Kurcinski","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B17","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkw329","article-title":"PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex","volume":"44","author":"Lamiable","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B18","doi-asserted-by":"crossref","first-page":"W299","DOI":"10.1093\/nar\/gki370","article-title":"ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures","volume":"33","author":"Landau","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B19","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1002\/prot.24422","article-title":"Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions","volume":"81","author":"Lavi","year":"2013","journal-title":"Proteins"},{"key":"2023013110261057300_btaa005-B20","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkv495","article-title":"GalaxyPepDock: a protein\u2013peptide docking tool based on interaction similarity and energy optimization","volume":"43","author":"Lee","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B21","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1002\/prot.24428","article-title":"Docking, scoring, and affinity prediction in CAPRI","volume":"81","author":"Lensink","year":"2013","journal-title":"Proteins"},{"key":"2023013110261057300_btaa005-B22","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1101\/gad.240531.114","article-title":"Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3\/H4 heterodimer by the Hat1p\/Hat2p complex","volume":"28","author":"Li","year":"2014","journal-title":"Genes Dev"},{"key":"2023013110261057300_btaa005-B23","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1021\/acs.jcim.8b00777","article-title":"Spot-peptide: template-based prediction of peptide-binding proteins and peptide-binding sites","volume":"59","author":"Litfin","year":"2019","journal-title":"J. Chem. Inf. Model"},{"key":"2023013110261057300_btaa005-B24","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1093\/molbev\/msh194","article-title":"Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior","volume":"21","author":"Mayrose","year":"2004","journal-title":"Mol. Biol. Evol"},{"key":"2023013110261057300_btaa005-B25","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2164-10-S1-S12","article-title":"Protein disorder in the human diseasome: unfoldomics of human genetic diseases","volume":"10","author":"Midic","year":"2009","journal-title":"BMC Genomics"},{"key":"2023013110261057300_btaa005-B26","doi-asserted-by":"crossref","first-page":"i787","DOI":"10.1093\/bioinformatics\/bty587","article-title":"Topology independent structural matching discovers novel templates for protein interfaces","volume":"34","author":"Mirabello","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013110261057300_btaa005-B27","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/j.jmb.2006.07.087","article-title":"Analysis of molecular recognition features (MoRFs)","volume":"362","author":"Mohan","year":"2006","journal-title":"J. Mol. Biol"},{"key":"2023013110261057300_btaa005-B28","doi-asserted-by":"crossref","first-page":"e405","DOI":"10.1371\/journal.pbio.0030405","article-title":"Systematic discovery of new recognition peptides mediating protein interaction networks","volume":"3","author":"Neduva","year":"2005","journal-title":"PLoS Biol"},{"key":"2023013110261057300_btaa005-B29","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.molcel.2015.05.017","article-title":"Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape and phenotypic features of mouse ESCs","volume":"59","author":"Noh","year":"2015","journal-title":"Mol. Cell"},{"key":"2023013110261057300_btaa005-B30","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res"},{"key":"2023013110261057300_btaa005-B31","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.copbio.2008.06.004","article-title":"Peptide-mediated interactions in biological systems: new discoveries and applications","volume":"19","author":"Petsalaki","year":"2008","journal-title":"Curr. Opin. Biotechnol"},{"key":"2023013110261057300_btaa005-B32","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1093\/bioinformatics\/btu097","article-title":"ZDOCK server: interactive docking prediction of protein\u2013protein complexes and symmetric multimers","volume":"30","author":"Pierce","year":"2014","journal-title":"Bioinformatics"},{"key":"2023013110261057300_btaa005-B33","doi-asserted-by":"crossref","first-page":"D219","DOI":"10.1093\/nar\/gkw1056","article-title":"DisProt 7.0: a major update of the database of disordered proteins","volume":"45","author":"Piovesan","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B34","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1002\/prot.22716","article-title":"Sub-angstrom modeling of complexes between flexible peptides and globular proteins","volume":"78","author":"Raveh","year":"2010","journal-title":"Proteins"},{"key":"2023013110261057300_btaa005-B35","volume-title":"Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models","author":"Rhodes","year":"2010"},{"key":"2023013110261057300_btaa005-B36","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1016\/j.str.2015.05.021","article-title":"Fully blind peptide\u2013protein docking with pepATTRACT","volume":"23","author":"Schindler","year":"2015","journal-title":"Structure"},{"key":"2023013110261057300_btaa005-B37","author":"Schr\u00f6dinger","year":"2015"},{"key":"2023013110261057300_btaa005-B38","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.str.2007.11.016","article-title":"Protein structure fitting and refinement guided by cryo-EM density","volume":"16","author":"Topf","year":"2008","journal-title":"Structure"},{"key":"2023013110261057300_btaa005-B39","doi-asserted-by":"crossref","first-page":"W423","DOI":"10.1093\/nar\/gks398","article-title":"PepSite: prediction of peptide-binding sites from protein surfaces","volume":"40","author":"Trabuco","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023013110261057300_btaa005-B40","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1016\/j.bbagrm.2014.06.002","article-title":"Myc and its interactors take shape","volume":"1849","author":"Tu","year":"2015","journal-title":"Biochim. Biophys. Acta"},{"key":"2023013110261057300_btaa005-B41","doi-asserted-by":"crossref","first-page":"2351","DOI":"10.1021\/pr0701411","article-title":"Characterization of molecular recognition features, MoRFs, and their binding partners","volume":"6","author":"Vacic","year":"2007","journal-title":"J. Proteome Res"},{"key":"2023013110261057300_btaa005-B42","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1002\/prot.25280","article-title":"InterPred: a pipeline to identify and model protein\u2013protein interactions","volume":"85","author":"Wallner","year":"2017","journal-title":"Proteins"},{"key":"2023013110261057300_btaa005-B43","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1051\/epn\/19861701011","article-title":"NMR with proteins and nucleic acids","volume":"17","author":"W\u00fcthrich","year":"1986","journal-title":"Europhys. News"},{"key":"2023013110261057300_btaa005-B44","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/jcc.23771","article-title":"Predicting peptide binding sites on protein surfaces by clustering chemical interactions","volume":"36","author":"Yan","year":"2015","journal-title":"J. Comput. Chem"},{"key":"2023013110261057300_btaa005-B45","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1093\/nar\/gki524","article-title":"TM-Align: a protein structure alignment algorithm based on the TM-score","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa005\/32219447\/btaa005.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/8\/2458\/48985055\/bioinformatics_36_8_2458.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/8\/2458\/48985055\/bioinformatics_36_8_2458.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:29:26Z","timestamp":1675196966000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/8\/2458\/5698698"}},"subtitle":[],"editor":[{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,1,9]]},"references-count":45,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2020,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa005","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,4,15]]},"published":{"date-parts":[[2020,1,9]]}}}