Enviaments recents

  • 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
  • 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)
    Article
    Accés restringit per política de l'editorial
    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 ...
  • Enhancing backbone sampling in Monte Carlo simulations using Internal Coordinates Normal Mode Analysis 

    Gil, Victor A.; Lecina, Daniel; Grebner, Christoph; Guallar, Victor (Elsevier, 2016-07-04)
    Article
    Accés restringit per política de l'editorial
    Normal mode methods are becoming a popular alternative to sample the conformational landscape of proteins. In this study, we describe the implementation of an internal coordinate normal mode analysis method and its application ...
  • Computer-aided laccase engineering: toward biological oxidation of arylamines 

    Santiago, Gerard; de Salas, Felipe; Lucas, Fatima; Monza, Emanuele; Acebes, Sandra; Martinez, Ángel T.; Camarero, Susana (ACS Publications, 2016-07-08)
    Article
    Accés restringit per política de l'editorial
    Oxidation of arylamines, such as aniline, is of high industrial interest and laccases have been proposed as biocata-lysts to replace harsh chemical oxidants. However, the reaction is hampered by the redox potential of the ...
  • Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer 

    Heyn, Holger; Vidal, Enrique; Ferreira, Humberto J.; Vizoso, Miguel; Sayols, Sergi; Gomez, Antonio; Moran, Sebastian; Boque-Sastre, Raquel; Guil, Sonia; Martinez-Cardus, Anna; Lin, Charles Y.; Romina, Royo; Sanchez-Mut, Jose V.; Martinez, Ramon; Gut, Marta; Torrents, David; Orozco, Modesto; Gut, Ivo; Young, Richard A.; Esteller, Manel (BioMed Central, 2016-01-26)
    Article
    Accés obert
    Background One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. ...

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