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The International Journal of Robotics Research, Vol. 24, No. 2-3, 131-150 (2005)
DOI: 10.1177/0278364905050358
© 2005 SAGE Publications

Multiple Docking for Protein Structure Prediction

Yuval Inbar

School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel, inbaryuv{at}tau.ac.il

Haim J. Wolfson

School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel

Ruth Nussinov

Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel and Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology, NCI - FCRDC, Bldg 469, Rm 151, Frederick, MD 21702, USA

Protein structure prediction and protein docking prediction are two related problems in molecular biology. We suggest the use of multiple docking in the process of protein structure prediction. Once reliable structural models are predicted to disjoint fragments of the protein target sequence, a combinatorial assembly may be used to predict their native arrangement. Here, we present CombDock, a combinatorial docking algorithm for the structural units assembly problem. We have tested the algorithm on various examples using both domains and domain substructures as input. Inaccurate models of the structural units were also used, to test the robustness of the algorithm. The algorithm was able to predict a near-native arrangement of the input structural units in almost all of the cases, showing that the combinatorial approach succeeds in overcoming the inexact shape complementarity caused by the inaccuracy of the models.

Key Words: protein structure prediction • multiple docking • combinatorial assembly • self-reconfigurable chain-type system


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