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Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark.
Kastritis PL, Bonvin AM. Kastritis PL, et al. J Proteome Res. 2010 May 7;9(5):2216-25. doi: 10.1021/pr9009854. J Proteome Res. 2010. PMID: 20329755
Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.
Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM. Vangone A, et al. Among authors: kastritis pl. Proteins. 2017 Mar;85(3):417-423. doi: 10.1002/prot.25198. Epub 2016 Nov 24. Proteins. 2017. PMID: 27802573 Free PMC article.
Defining the limits of homology modeling in information-driven protein docking.
Rodrigues JP, Melquiond AS, Karaca E, Trellet M, van Dijk M, van Zundert GC, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AM. Rodrigues JP, et al. Among authors: kastritis pl. Proteins. 2013 Dec;81(12):2119-28. doi: 10.1002/prot.24382. Epub 2013 Oct 17. Proteins. 2013. PMID: 23913867
Clustering biomolecular complexes by residue contacts similarity.
Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. Rodrigues JP, et al. Proteins. 2012 Jul;80(7):1810-7. doi: 10.1002/prot.24078. Epub 2012 May 8. Proteins. 2012. PMID: 22489062
dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.
Spiliotopoulos D, Kastritis PL, Melquiond AS, Bonvin AM, Musco G, Rocchia W, Spitaleri A. Spiliotopoulos D, et al. Among authors: kastritis pl. Front Mol Biosci. 2016 Aug 31;3:46. doi: 10.3389/fmolb.2016.00046. eCollection 2016. Front Mol Biosci. 2016. PMID: 27630991 Free PMC article.
Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.
Kastritis PL, van Dijk AD, Bonvin AM. Kastritis PL, et al. Methods Mol Biol. 2012;819:355-74. doi: 10.1007/978-1-61779-465-0_22. Methods Mol Biol. 2012. PMID: 22183547
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Lensink MF, et al. Among authors: kastritis pl. Proteins. 2016 Sep;84 Suppl 1(Suppl Suppl 1):323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1. Proteins. 2016. PMID: 27122118 Free PMC article.
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. Xue LC, et al. Among authors: kastritis pl. Bioinformatics. 2016 Dec 1;32(23):3676-3678. doi: 10.1093/bioinformatics/btw514. Epub 2016 Aug 8. Bioinformatics. 2016. PMID: 27503228
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Vreven T, et al. Among authors: kastritis pl. J Mol Biol. 2015 Sep 25;427(19):3031-41. doi: 10.1016/j.jmb.2015.07.016. Epub 2015 Jul 29. J Mol Biol. 2015. PMID: 26231283 Free PMC article.
Non-interacting surface solvation and dynamics in protein-protein interactions.
Visscher KM, Kastritis PL, Bonvin AM. Visscher KM, et al. Among authors: kastritis pl. Proteins. 2015 Mar;83(3):445-58. doi: 10.1002/prot.24741. Epub 2015 Jan 21. Proteins. 2015. PMID: 25524313
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