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Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Rocco Moretti 1, 2 Sarel J Fleishman 3, 2 Rudi Agius 2, 4 Mieczyslaw Torchala 2, 4 Paul A. Bates 4 Panagiotis L Kastritis 5 João P. G. L. M. Rodrigues 5 Mikael Trellet 5 Alexandre M. J. J. Bonvin 5 Meng Cui 6 Marianne Rooman 7 Dimitri Gillis 8 Yves Dehouck 9 Iain Moal 10 Miguel Romero-Durana 10 Laura Pérez-Cano 10 Chiara Pallara 10 Brian Jimenez 10 Juan Fernández-Recio 10 Samuel C Flores 11 Michael Pacella 12 Krishna Praneeth Kilambi 12 Jeffrey J Gray 12 Petr Popov 13, 2 Sergei Grudinin 2, 13, * Juan Esquivel-Rodríguez 14 Daisuke Kihara 14 Nan Zhao 15 Dmitry Korkin 15 Xiaolei Zhu 16 Omar N A Demerdash 16 Julie Mitchell 16 Eiji Kanamori 17 Yuko Tsuchiya 18 Haruki Nakamura 19 Hasup Lee 20 Hahnbeom Park 20 Chaok Seok 20 Jamica Sarmiento 19 Shide Liang 19 Shusuke Teraguchi 19 Daron M Standley 19 Hiromitsu Shimoyama 21 Genki Terashi 21 Mayuko Takeda-Shitaka 21 Mitsuo Iwadate 22 Hideaki Umeyama 22 Dmitri Beglov 23 David R Hall 23 Dima Kozakov 23 Sandor Vajda 23 Brian G Pierce 24 Howook Hwang 24 Thom Vreven 24 Zhiping Weng 24 Yangyu Huang 25 Haotian Li 25 Xiufeng Yang 25 Xiaofeng Ji 25 Shiyong Liu 25 Yi Xiao 25 Martin Zacharias 26 Sanbo Qin 27 Huan-Xiang Zhou 27 Sheng-You Huang 15 Xiaoqin Zou 15 Sameer Velankar 28 Joel Janin 29 Shoshana J Wodak 30, 31 David Baker 1 
* Corresponding author
13 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology
Abstract : Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.
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Submitted on : Monday, November 18, 2013 - 4:41:31 PM
Last modification on : Friday, November 18, 2022 - 9:25:00 AM

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Rocco Moretti, Sarel J Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, et al.. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins - Structure, Function and Bioinformatics, 2013, 81 (11), pp.1980 - 1987. ⟨10.1002/prot.24356⟩. ⟨hal-00905794⟩



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