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Page 1
Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55.
Reys V, Giulini M, Cojocaru V, Engel A, Xu X, Roel-Touris J, Geng C, Ambrosetti F, Jiménez-García B, Jandova Z, Koukos PI, van Noort C, Teixeira JMC, van Keulen SC, Réau M, Honorato RV, Bonvin AMJJ. Reys V, et al. Among authors: jimenez garcia b. Proteins. 2024 Dec 30. doi: 10.1002/prot.26789. Online ahead of print. Proteins. 2024. PMID: 39739354
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.
Honorato RV, Trellet ME, Jiménez-García B, Schaarschmidt JJ, Giulini M, Reys V, Koukos PI, Rodrigues JPGLM, Karaca E, van Zundert GCP, Roel-Touris J, van Noort CW, Jandová Z, Melquiond ASJ, Bonvin AMJJ. Honorato RV, et al. Among authors: jimenez garcia b. Nat Protoc. 2024 Nov;19(11):3219-3241. doi: 10.1038/s41596-024-01011-0. Epub 2024 Jun 17. Nat Protoc. 2024. PMID: 38886530 Review.
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Vela… See abstract for full author list ➔ Lensink MF, et al. Among authors: jimenez garcia b. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
UDock2: interactive real-time multi-body protein-protein docking software.
Plateau-Holleville C, Guionnière S, Boyer B, Jiménez-Garcia B, Levieux G, Mérillou S, Maria M, Montes M. Plateau-Holleville C, et al. Among authors: jimenez garcia b. Bioinformatics. 2022 Jan 1;39(10):btad609. doi: 10.1093/bioinformatics/btad609. Bioinformatics. 2022. PMID: 37792496 Free PMC article.
Functional performance recovery after individualized nutrition therapy combined with a patient-tailored physical rehabilitation program versus standard physiotherapy in patients with long COVID: a pilot study.
Roggeman S, Jimenez Garcia BG, Leemans L, Demol J, Geers J, De Smedt A, Putman K, Schiltz M, Beckwée D, De Waele E. Roggeman S, et al. Among authors: jimenez garcia bg. Pilot Feasibility Stud. 2023 Sep 28;9(1):166. doi: 10.1186/s40814-023-01392-1. Pilot Feasibility Stud. 2023. PMID: 37759324 Free PMC article.
Towards design of drugs and delivery systems with the Martini coarse-grained model.
Kjølbye LR, Pereira GP, Bartocci A, Pannuzzo M, Albani S, Marchetto A, Jiménez-García B, Martin J, Rossetti G, Cecchini M, Wu S, Monticelli L, Souza PCT. Kjølbye LR, et al. Among authors: jimenez garcia b. QRB Discov. 2022 Oct 12;3:e19. doi: 10.1017/qrd.2022.16. eCollection 2022. QRB Discov. 2022. PMID: 37529288 Free PMC article. Review.
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.
Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LA, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin AMJJ, Savojardo C, Martelli PL, Casadio R, Tubiana J, Wolfson HJ, Oliva R, Barradas-Bautista D, Ricciardelli T, Cavallo L, Venclovas Č, Olechnovič K, Guerois R, Andreani J, Martin J, Wang X, Terashi G, Sarkar D, Christoffer C, Aderinwale T, Verburgt J, Kihara D, Marchand A, Correia BE, Duan R, Qiu L, Xu X, Zhang S, Zou X, Dey S, Dunbrack RL, Levy ED, Wodak SJ. Schweke H, et al. Among authors: jimenez garcia b. Proteomics. 2023 Sep;23(17):e2200323. doi: 10.1002/pmic.202200323. Epub 2023 Jun 27. Proteomics. 2023. PMID: 37365936 Free PMC article.
42 results