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Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ. Kurkcuoglu Z, et al. Among authors: xue lc. J Comput Aided Mol Des. 2018 Jan;32(1):175-185. doi: 10.1007/s10822-017-0049-y. Epub 2017 Aug 22. J Comput Aided Mol Des. 2018. PMID: 28831657 Free PMC article.
The solution structure of the kallikrein-related peptidases inhibitor SPINK6.
Jung S, Fischer J, Spudy B, Kerkow T, Sönnichsen FD, Xue L, Bonvin AM, Goettig P, Magdolen V, Meyer-Hoffert U, Grötzinger J. Jung S, et al. Biochem Biophys Res Commun. 2016 Feb 26;471(1):103-8. doi: 10.1016/j.bbrc.2016.01.172. Epub 2016 Jan 30. Biochem Biophys Res Commun. 2016. PMID: 26828269 Free PMC article.
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. 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.
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: xue lc. Proteins. 2017 Mar;85(3):417-423. doi: 10.1002/prot.25198. Epub 2016 Nov 24. Proteins. 2017. PMID: 27802573 Free PMC article.
Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418).
Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Vangone A, et al. Among authors: xue lc. Proteins. 2017 Aug;85(8):1589-1590. doi: 10.1002/prot.25339. Proteins. 2017. PMID: 28730688 Free PMC article. No abstract available.
31 results