Enviaments recents

  • 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 ...
  • 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 restringit per política de l'editorial
    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. ...
  • Challenges of docking in large, flexible and promiscuous binding sites 

    Kotev, Martin; Soliva, Robert; Orozco, Modesto (Elsevier, 2016-10-15)
    Article
    Accés restringit per política de l'editorial
    After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; ...
  • The unravelling of the complex pattern of tyrosinase inhibition 

    Deri, Batel; Kanteev, Margarita; Goldfeder, Mor; Lecina, Daniel; Guallar, Victor; Adir, Noam; Fishman, Ayelet (Nature Publishing Group, 2016-10-11)
    Article
    Accés obert
    Tyrosinases are responsible for melanin formation in all life domains. Tyrosinase inhibitors are used for the prevention of severe skin diseases, in skin-whitening creams and to avoid fruit browning, however continued use ...
  • Ecoupling server: A tool to compute and analyze electronic couplings 

    Cabeza de Vaca, Israel; Acebes, Sandra; Guallar, Victor (Wiley Online Library, 2016-05-08)
    Article
    Accés obert
    Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to ...
  • How experiments and molecular simulations can help understand selective C25-hydroxylation of vitamin D by fungal peroxygenases 

    Lucas, Fatima; Babot, Esteban D.; Cañellas, Marina; del Río, José C.; Kalum, Lisbeth; Ullrich, René; Hofrichter, Martin; Martínez, Angel T.; Gutiérrez, Ana (2016-02-01)
    Comunicació de congrés
    Accés obert

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