• Blind prediction of interfacial water positions in CAPRI 

    Lensink, Marc F.; Moal, Iain H.; Bates, Paul A.; Kastritis, Panagiotis L.; Melquiond, Adrien S.J.; Karaca, Ezgi; Schmitz, Christophe; van Dijk, Marc; Bonvin, Alexandre M.J.J.; Eisenstein, Miriam; Jiménez-Garcia, Brian; Grosdidier, Solène; Solernou, Albert; Pérez-Cano, Laura; Pallara, Chiara; Fernández-Recio, Juan; Xu, Jianqing; Muthu, Pravin; Kilambi, Krishna P.; Gray, Jeffrey J.; Grudinin, Sergei; Derevyanko, Georgy; Mitchell, Julie C.; Wieting, John; Kanamori, Eiji; Tsuchiya, Yuko; Murakami, Yoichi; Sarmiento, Joy; Standley, Daron M.; Shirota, Matsuyuki; Kinoshita, Kengo; Nakamura, Haruki; Chavent, Matthieu; Ritchie, David W.; Park, Hahnbeom; Ko, Junsu; Lee, Hasup; Seok, Chaok; Shen, Yang; Kozakov, Dima; Vajda, Sandor; Kundrotas, Petras J.; Vakser, Ilya A.; Pierce, Brian G.; Hwang, Howook; Vreven, Thom; Weng, Zhiping; Buch, Idit; Farkash, Efrat; Wolfson, Haim J.; Zacharias, Martin; Qin, Sanbo; Zhou, Huan-Xiang; Huang, Shen-You; Zou, Xiaoqin; Wojdyla, Justyna A.; Kleanthous, Colin; Wodak, Shoshana J. (Wiley, 2014-04)
    Article
    Accés obert
    We report the first assessment of blind predictions of water positions at protein–protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting ...
  • Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein–Protein Encounters 

    Pallara, Chiara; Rueda, Manuel; Abagyan, Ruben; Fernández-Recio, Juan (American Chemical Society, 2016-06-20)
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    Accés obert
    To understand cellular processes at the molecular level we need to improve our knowledge of protein−protein interactions, from a structural, mechanistic, and energetic point of view. Current theoretical studies and ...
  • Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor 

    Bernal-Bayard, Pilar; Pallara, Chiara; Castell, M. Carmen; Molina-Heredia, Fernando P.; Fernández-Recio, Juan; Hervás, Manuel; Navarro, José A. (Elsevier, 2015-12)
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    In the Phaeodactylum tricornutum alga, as in most diatoms, cytochrome c6 is the only electron donor to photosystem I, and thus they lack plastocyanin as an alternative electron carrier. We have investigated, by using ...
  • Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases 

    Ordan, Merav; Pallara, Chiara; Maik-Rachline, Galia; Hanoch, Tamar; Gervasio, Francesco L.; Glaser, Fabian; Fernandez-Recio, Juan; Seger, Rony (Nature Publishing Group, 2018-08-07)
    Article
    Accés obert
    MAPK/ERK kinase (MEK) 1/2 are central signaling proteins that serve as specificity determinants of the MAPK/ERK cascade. More than twenty activating mutations have been reported for MEK1/2, and many of them are known to ...
  • Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment 

    Lesink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy; Huang, Shen-You; Schneidman-Duhovny, Dina; Sali, Andrej; Segura, Joan; Fernandez-Fuentes, Narcis; Shruthi, Viswanath; Elber, Ron; Grudinin, Sergei; Popov, Petr; Neveu, Emilie; Lee, Hasup; Baek, Minkyung; Park, Sangwoo; Heo, Lim; Lee, Gyu R.; Seok, Chaok; Qin, Sanbo; Zhou, Huan-Xiang; Ritchie, David W.; Maigret, Bernard; Devignes, Marie-Dominique; Ghoorah, Anisah; Torchala, Mieczyslaw; Chaleil, Raphaël A.G.; Bates, Paul A.; Ben-Zeev, Efrat; Eisenstein, Miriam; Negi, Surendra S.; Weng, Zhiping; Vreven, Thom; Pierce, Brian G.; Borrman, Tyler M.; Yu, Jinchao; Ochsenbein, Françoise; Guerois, Raphaël; Vangone, Anna; Rodrigues, Joao P.G.L.M.; Zundert, Gydo van; Nellen, Mehdi; Xue, Li; Karaca, Ezgi; Melquiond, Adrien S.J.; Visscher, Koen; Kastritis, Panagiotis L.; Bonvin, Alexandre M.J.J.; Xianjin, Xu; Qiu, Liming; Yan, Chengfei; Li, Jilong; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Shen, Yang; Peterson, Lenna X.; Kim, Hyung-Rae; Roy, Amit; Han, Xusi; Esquivel-Rodriguez, Juan; Kihara, Daisuke; Yu, Xiaofeng; Bruce, Neil J.; Fuller, Jonathan C.; Wade, Rebecca C.; Anishchenko, Ivan; Kundrotas, Petras J.; Vakser, Ilya A.; Imai, Kenichiro; Yamada, Kazunori; Oda, Toshiyuki; Nakamura, Tsukasa; Tomii, Kentaro; Pallara, Chiara; Romero-Durana, Miguel; Jiménez-García, Brian; Moal, Iain H.; Fernández-Recio, Juan; Joung, Jong Y.; Kim, Jong Y.; Joo, Keehyoung; Lee, Jooyoung; Kozakov, Dima; Vajda, Sandor; Mottarella, Scott; Hall, David R.; Beglov, Dmitri; Mamonov, Artem; Xia, Bing; Bohnuud, Tanggis; del Carpio, Carlos A.; Ichiishi, Eichiro; Marze, Nicholas; Kuroda, Daisuke; Burman, Shourya S.; Gray, Jeffrey J.; Chermak, Edrisse; Cavallo, Luigi; Oliva, Romina; Tovchigrechko, Andrey; Wodak, Shoshana J. (Wiley, 2016-06-01)
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    We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets ...
  • pyDock performance in 5th CAPRI edition: from docking and scoring to binding affinity predictions and other challenges 

    Pallara, Chiara; Jiménez-García, Brian; Romero, Miguel; Fernandez-Recio, Juan (Barcelona Supercomputing Center, 2015-05-05)
    Text en actes de congrés
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    Proteins form the executive machinery underlying all the biological processes that occur within and between cells, from DNA replication to protein degradation. Although genome-scale technologies enable to clarify their ...
  • pyDock scoring for the new modeling challenges in docking: protein-peptide, homo-multimers and domain-domain interactions 

    Pallara, Chiara; Jiménez-García, Brian; Romero, Miguel; Moal, Iain H.; Fernández-Recio, Juan (Wiley, 2016-10-04)
    Article
    Accés obert
    The 6th CAPRI edition included new modelling challenges, such as the prediction of protein-peptide complexes, and the modelling of homo-oligomers and domain-domain interactions as part of the first joint CASP-CAPRI experiment. ...
  • Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems 

    Barradas-Bautista, Didier; Rosell, Mireia; Pallara, Chiara; Fernández-Recio, Juan (Academic Press, 2018)
    Capítol de llibre
    Accés obert
    A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains ...