Now showing items 1-9 of 9

  • 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 ...
  • 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 ...
  • 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 ...
  • 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)
    Conference report
    Open Access
    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 ...
  • 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 ...
  • 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
    Open Access
    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. ...
  • SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation 

    Jankauskaite, Justina; Jiménez-García, Brian; Dapkunas, Justas; Fernández-Recio, Juan; Moal, Iain H. (Oxford University Press, 2018-07-18)
    Article
    Open Access
    Motivation: Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the ...
  • Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2 

    Vreven, Thom; Moal, Iain H.; Vangone, Anna; Pierce, Brian G.; Kastritis, Panagiotis L.; Torchala, Mieczyslaw; Chaleil, Raphael; Jiménez-García, Brian; Bates, Paul A.; Fernández-Recio, Juan; Bonvin, Alexandre M. J. J.; Weng, Zhiping (Elsevier, 2015-09-25)
    Article
    Open Access
    We present an updated and integrated version of our widely used protein–protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein–protein complexes along ...