Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies Yuval Inbar 1, Hadar Benyamini 2, Ruth Nussinov.

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Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies Yuval Inbar 1, Hadar Benyamini 2, Ruth Nussinov 2,3 and Haim J Wolfson 1. J. Phys. Biol. 2 (2005) S156-S165 1 School of Computer Science, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel 2 Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel 3 Basic Research Program, SAIC - Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Bldg 469, Rm 151 Frederick, MD 21702, USA Presented by Greg Goldgof

Purpose of CombDock  To predict spatial arrangement of several subunits  Domain Assembly  Subunits: connected protein domains  Multi-Molecular Assembly  Subunits: separated protein chains  The algorithm cannot predict whether a given set of subunits actually bind to each other to form a single complex.  Assuming the subunits do form a complex, the program can predict a near-native assembly and to suggest it as one of the most preferable hypotheses.

Algorithm Flow  Predict pairwise interactions between each pair of subunits.  A dissection algorithm was used to cut protein structures into compact and stable substructures.  Combine different predicted pairwise interactions to produce a large set of candidate complexes.  Score solutions.  Cluster similar solutions to avoid redundancy.

Performance  Performance is gauged by RMSD from known structure, rank of score, and runtime.