Presented by Greg Goldgof

1. Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies 1 School of Computer Science, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel2 Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel3 Basic Research Program, SAIC - Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Bldg 469, Rm 151 Frederick, MD 21702, USA Yuval Inbar1, Hadar Benyamini2, Ruth Nussinov2,3 and  Haim J Wolfson1. J. Phys. Biol. 2 (2005) S156-S165 Presented by Greg Goldgof

2. 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.

3. 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.

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