Docking of protein molecular surfaces with evolutionary trace analysis

We have developed a new method to predict protein– protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2007-12, Vol.69 (4), p.832-838
Main Authors: Kanamori, Eiji, Murakami, Yoichi, Tsuchiya, Yuko, Standley, Daron M., Nakamura, Haruki, Kinoshita, Kengo
Format: Article
Language:English
Subjects:
3D structure
Algorithms
CAPRI
computational biology
Computational Biology - methods
Computer Simulation
Crystallography, X-Ray - methods
Databases, Protein
Dimerization
Evolution, Molecular
Imaging, Three-Dimensional
Monte Carlo Method
prediction of protein complex
Protein Binding
Protein Conformation
Protein Interaction Mapping
protein-protein interaction
Proteins - chemistry
Proteomics - methods
shape complementarity
Software
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Summary:We have developed a new method to predict protein– protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of shape complementarity weighted by the conservation of the interacting residues. The optimization is carried out using a genetic algorithm in combination with Monte Carlo sampling. We applied this method to CAPRI targets and evaluated the performance systematically. Consequently, our method could achieve native‐like predictions in several cases. In addition, we have analyzed the feasibility of the ET method for docking simulations, and found that the conservation information was useful only in a limited category of proteins (signal related proteins and enzymes). Proteins 2007. © 2007 Wiley‐Liss, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/prot.21737