Now showing items 1-10 of 10

    • 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 ...
    • 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 ...
    • 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. ...
    • 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 ...
    • 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 ...
    • Structural characterization of protein–protein interactions with pyDockSAXS 

      Jiménez-García, Brian; Bernadó, Pau; Fernández-Recio, Juan (Humana Press, 2020)
      Part of book or chapter of book
      Open Access
      Structural characterization of protein–protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical ...
    • 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 ...