Now showing items 1-12 of 12

  • 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-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 ...
  • 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 ...
  • 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 ...
  • 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.
  • 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 ...
  • 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 ...
  • 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 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 ...