Multiple docking for protein structure prediction

Yuval Inbar*, Haim J. Wolfson, Ruth Nussinov

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


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.

Original languageEnglish
Pages (from-to)131-150
Number of pages20
JournalInternational Journal of Robotics Research
Issue number2-3
StatePublished - Feb 2005


  • Combinatorial assembly
  • Multiple docking
  • Protein structure prediction
  • Self-reconfigurable chain-type system


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