Now showing items 1-20 of 26

  • Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction 

    Somajo, Sofía; Ahnström, Josefin; Fernández-Recio, Juan; Gierula, Magdalena; Villoutreix, Bruno O.; Dahlbäck, Björn (Schattauer, 2015-05)
    Article
    Open Access
    Protein S functions as a cofactor for tissue factor pathway inhibitor (TFPI) and activated protein C (APC). The sex hormone binding globulin (SHBG)-like region of protein S, consisting of two laminin G-like domains (LG1 ...
  • A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining 

    Barradas-Bautista, Didier; Moal, Iain H.; Fernández-Recio, Juan (Wiley, 2017-07)
    Article
    Open Access
    Protein-protein interactions play fundamental roles in biological processes including signaling, metabolism, and trafficking. While the structure of a protein complex reveals crucial details about the interaction, it is ...
  • 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
    Open Access
    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 ...
  • CCharPPI web server: computational characterization of protein–protein interactions from structure 

    Moal, Iain H.; Jiménez-García, Brian; Fernández-Recio, Juan (Oxford Journals, 2015-01-01)
    Article
    Open Access
    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 ...
  • 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
    Open Access
    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 ...
  • Characteritzation of pathological mutations affecting protein-protein interactions for drug discovery 

    Rosell, Mireia; Fernández-Recio, Juan (Barcelona Supercomputing Center, 2018-04-24)
    Conference report
    Open Access
  • Comment on ‘protein–protein binding affinity prediction from amino acid sequence 

    Moal, Iain H.; Fernández-Recio, Juan (2014-10-17)
    Article
    Open Access
    Predicting the strength of interactions between globular proteins is a central and important topic in structural bioinformatics (Moal et al., 2013). The amino acid sequence represents the chemical bonding in a protein ...
  • 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
    Open Access
    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 ...
  • Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations 

    Barradas-Bautista, Didier; Fernández-Recio, Juan (Public Library of Science, 2017-08-25)
    Article
    Open Access
    Next-generation sequencing (NGS) technologies are providing genomic information for an increasing number of healthy individuals and patient populations. In the context of the large amount of generated genomic data that is ...
  • Docking through democracy re-ranking protein-protein decoys with a voting system 

    Barradas-Bautista, Didier; Moal, Iain H.; Fernández-Recio, Juan (Barcelona Supercomputing Center, 2015-05-05)
    Conference report
    Open Access
    We have develop a machine learning framework to enhance protein-protein docking results, using Schulze voting method applied to several models from Support Vector machines.
  • EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGF 

    Khayati, Farah; Pérez-Cano, Laura; Maouche, Kamel; Sadoux, Aurélie; Boutalbi, Zineb; Podgorniak, Marie-Pierre; Maskos, Uwe; Setterblad, Niclas; Janin, Anne; Calvo, Fabien; Lebbé, Céleste; Menashi, Suzanne; Fernández-Recio, Juan; Mourah, Samia (Wiley, 2015-03-23)
    Article
    Open Access
    EMMPRIN/CD147 is mainly known for its protease inducing function but a role in promoting tumor angiogenesis has also been demonstrated. This study provides evidence that EMMPRIN is a new coreceptor for the VEGFR-2 tyrosine ...
  • Hot-spot analysis for drug discovery targeting protein-protein interactions 

    Rosell, Mireia; Fernández-Recio, Juan (Taylor & Francis, 2018-01-29)
    Article
    Open Access
    Introduction: Protein-protein interactions are important for biological processes and pathological situations, and are attractive targets for drug discovery. However, rational drug design targeting protein-protein interactions ...
  • Inferring the microscopic surface energy of protein-protein interfaces from mutation data 

    Moal, Iain H.; Dapkūnas, Justas; Fernández-Recio, Juan (Wiley, 2015-04)
    Article
    Open Access
    Mutations at protein-protein recognition sites alter binding strength by altering the chemical nature of the interacting surfaces. We present a simple surface energy model, parameterised with empirical DDG values, yielding ...
  • 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)
    Article
    Open Access
    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 ...
  • IRaPPA: information retrieval based integration of biophysical models for protein assembly selection 

    Moal, Iain H.; Barradas-Bautista, Didier; Jiménez-Garcia, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A.; Fernández-Recio, Juan (Oxford University Press, 2017-02-14)
    Article
    Open Access
    Motivation: In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can ...
  • LightDock: a new multi-scale approach to protein–protein docking 

    Jiménez-García, Brian; Roel-Touris, Jorge; Romero-Durana, Miguel; Vidal-Piñol, Miquel; Jiménez-González, Daniel; Fernández-Recio, Juan (Oxford University Press, 2017-09-04)
    Article
    Open Access
    Computational prediction of protein–protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult ...
  • 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
    Open Access
    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 ...
  • 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
    Open Access
    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 ...
  • pyDockDNA: a new approach for protein-DNA docking 

    Rodríguez-Lumbreras, Luis Ángel; Jiménez-García, Brian; Fernández-Recio, Juan (Barcelona Supercomputing Center, 2017-05-04)
    Conference report
    Open Access
    Here we present pyDockDNA, which is based on the pyDock program, with a new module for reading and parsing DNA molecules. The protocol is composed of two major steps: sampling and scoring. The first sampling step consists ...
  • pyDockSAXS: protein–protein complex structure by SAXS and computational docking 

    Jiménez-García, Brian; Pons, Carles; Svergun, Dmitri I.; Bernadó, Pau; Fernández-Recio, Juan (Oxford Journals, 2015-07-01)
    Article
    Open Access
    Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques ...