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Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
Proteins. 2021 Dec;89(12):1800-1823. doi: 10.1002/prot.26222. Epub 2021 Sep 13.
Proteins. 2021.
PMID: 34453465
Free PMC article.
Modeling of Protein Complexes and Molecular Assemblies with pyDock.
Rosell M, Rodríguez-Lumbreras LA, Fernández-Recio J.
Rosell M, et al. Among authors: rodriguez lumbreras la.
Methods Mol Biol. 2020;2165:175-198. doi: 10.1007/978-1-0716-0708-4_10.
Methods Mol Biol. 2020.
PMID: 32621225
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Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Hon…
See abstract for full author list ➔
Lensink MF, et al. Among authors: rodriguez lumbreras la.
Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25.
Proteins. 2019.
PMID: 31612567
Free PMC article.
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Integrative modeling of protein-protein interactions with pyDock for the new docking challenges.
Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Jiménez-García B, Díaz L, Fernández-Recio J.
Rosell M, et al. Among authors: rodriguez lumbreras la.
Proteins. 2020 Aug;88(8):999-1008. doi: 10.1002/prot.25858. Epub 2019 Nov 30.
Proteins. 2020.
PMID: 31746039
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New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes.
Castell C, Rodríguez-Lumbreras LA, Hervás M, Fernández-Recio J, Navarro JA.
Castell C, et al. Among authors: rodriguez lumbreras la.
Plant Cell Physiol. 2021 Oct 29;62(7):1082-1093. doi: 10.1093/pcp/pcab044.
Plant Cell Physiol. 2021.
PMID: 33772595
Free PMC article.
Review.
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Structural vulnerability in EPCR suggests functional modulation.
Erausquin E, Rodríguez-Fernández A, Rodríguez-Lumbreras LÁ, Fernández-Recio J, Dichiara-Rodríguez MG, López-Sagaseta J.
Erausquin E, et al. Among authors: rodriguez lumbreras la.
Sci Rep. 2024 Jan 31;14(1):2591. doi: 10.1038/s41598-024-53160-7.
Sci Rep. 2024.
PMID: 38297105
Free PMC article.
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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: rodriguez lumbreras la.
Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31.
Proteins. 2023.
PMID: 37905971
Free PMC article.
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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: rodriguez lumbreras la.
Proteomics. 2023 Sep;23(17):e2200323. doi: 10.1002/pmic.202200323. Epub 2023 Jun 27.
Proteomics. 2023.
PMID: 37365936
Free PMC article.
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pyDockDNA: A new web server for energy-based protein-DNA docking and scoring.
Rodríguez-Lumbreras LA, Jiménez-García B, Giménez-Santamarina S, Fernández-Recio J.
Rodríguez-Lumbreras LA, et al.
Front Mol Biosci. 2022 Oct 6;9:988996. doi: 10.3389/fmolb.2022.988996. eCollection 2022.
Front Mol Biosci. 2022.
PMID: 36275623
Free PMC article.
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