Premium
Integrating statistical pair potentials into protein complex prediction
Author(s) -
Mintseris Julian,
Pierce Brian,
Wiehe Kevin,
Anderson Robert,
Chen Rong,
Weng Zhiping
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21502
Subject(s) - docking (animal) , macromolecular docking , computer science , casp , cluster analysis , computation , protein structure prediction , complementarity (molecular biology) , artificial intelligence , algorithm , machine learning , protein structure , chemistry , genetics , biology , medicine , biochemistry , nursing
The biophysical study of protein–protein interactions and docking has important implications in our understanding of most complex cellular signaling processes. Most computational approaches to protein docking involve a tradeoff between the level of detail incorporated into the model and computational power required to properly handle that level of detail. In this work, we seek to optimize that balance by showing that we can reduce the complexity of model representation and thus make the computation tractable with minimal loss of predictive performance. We also introduce a pair‐wise statistical potential suitable for docking that builds on previous work and show that this potential can be incorporated into our fast fourier transform‐based docking algorithm ZDOCK. We use the Protein Docking Benchmark to illustrate the improved performance of this potential compared with less detailed other scoring functions. Furthermore, we show that the new potential performs well on antibody‐antigen complexes, with most predictions clustering around the Complementarity Determining Regions of antibodies without any manual intervention. Proteins 2007. © 2007 Wiley‐Liss, Inc.