Enviaments recents

  • Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc 

    Rosell, Albert; Meury, Marcel; Alvarez-Marimon, Elena; Costa, Meritxell; Pérez-Cano, Laura; Zorzano, Antonio; Fernández-Recio, Juan; Palacín, Manuel; Fotiadis, Dimitrios (National Academy of Sciences, 2014-02-25)
    Article
    Accés obert
    Heteromeric amino acid transporters (HATs) are the unique example, known in all kingdoms of life, of solute transporters composed of two subunits linked by a conserved disulfide bridge. In metazoans, the heavy subunit is ...
  • CCharPPI web server: computational characterization of protein–protein interactions from structure 

    Moal, Iain H.; Jiménez-Garcia, Brian; Fernández-Recio, Juan (Oxford University Press, 2014-09-02)
    Article
    Accés obert
    The atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization ...
  • Optimization of protein–protein docking for predicting Fc–protein interactions 

    Agostino, Mark; Mancera, Ricardo L.; Ramsland, Paul A.; Fernández-Recio, Juan (Wiley, 2016-07-22)
    Article
    Accés restringit per política de l'editorial
    The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization ...
  • 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 ...
  • Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions 

    Grebner, Christoph; Lecina, Daniel; Gil, Victor; Ulander, Johan; Hansson, Pia; Dellsen, Anita; Tyrchan, Christian; Edman, Karl; Hogner, Anders; Guallar, Victor (Biophysical Society, 2017-03-28)
    Article
    Accés restringit per política de l'editorial
    In this study, we performed an extensive exploration of the ligand entry mechanism for members of the steroid nuclear hormone receptor family (androgen receptor, estrogen receptor α, glucocorticoid receptor, mineralocorticoid ...
  • The Multiple Roles of Waters in Protein Solvation 

    Hospital, Adam; Candotti, Michela; Gelpí, Josep Ll.; Orozco, Modesto (American Chemical Society, 2017-01-06)
    Article
    Accés restringit per política de l'editorial
    Extensive molecular dynamics (MD) simulations have been used to characterize the multiple roles of water in solvating different types of proteins under different environmental conditions. We analyzed a small set of proteins, ...
  • Physics-Based Visual Characterization of Molecular Interaction Forces 

    Hermosilla, Pedro; Estrada, Jorge; Guallar, Victor; Ropinski, Timo; Vinacua, Álvar; Vázquez, Pere-Pau (IEEE, 2017-01)
    Article
    Accés obert
    Molecular design procedures, such as drug design and protein engineering’ are complex processes, largely benefiting from computational resources but also from human analysis. In drug design, for example, a costly iterative ...
  • Active-Site-Directed Inhibitors of Prolyl Oligopeptidase Abolish Its Conformational Dynamics 

    López, Abraham; Herranz-Trillo, Fátima; Kotev, Martin; Gairí, Margarida; Guallar, Victor; Bernadó, Pau; Millet, Oscar; Tarragó, Teresa; Giralt, Ernest (Wiley, 2016-05-17)
    Article
    Accés restringit per política de l'editorial
    Deciphering conformational dynamics is crucial for understanding the biological functions of proteins and for designing compounds targeting them. In particular, providing an accurate description of microsecond–millisecond ...
  • Repurposing designed mutants: a valuable strategy for computer-aided laccase engineering – the case of POXA1b 

    Giacobelli, Valerio G.; Monza, Emanuele; Lucas, M. Fatima; Pezzella, Cinzia; Piscitelli, Alessandra; Guallar, Victor; Sannia, Giovanni (Royal Society of Chemistry, 2017-01-04)
    Article
    Accés restringit per política de l'editorial
    The broad specificity of laccases, a direct consequence of their shallow binding site, makes this class of enzymes a suitable template to build specificity toward putative substrates. In this work, a computational methodology ...
  • 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)
    Article
    Accés obert
    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 ...

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