|Y. Inbar, H.J. Wolfson
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact
Sciences, Tel Aviv University, Tel Aviv 69978, Israel and R. 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.