A New Approach to Rigid Body Minimization with Application to Molecular Docking.
Our work is motivated by energy minimization in the space of rigid affine transformations of macromolecules, an essential step in computational protein-protein docking. We introduce a novel representation of rigid body motion that leads to a natural formulation of the energy minimization problem as an optimization on the [Formula: see text] manifold, rather than the commonly usedSE(3). The new representation avoids the complications associated with optimization on theSE(3) manifold and provides additional flexibilities for optimization not available in that formulation. The approach is applicable to general rigid body minimization problems. Our computational results for a local optimization algorithm developed based on the new approach show that it is about an order of magnitude faster than a state of art local minimization algorithms for computational protein-protein docking.
Division of Systems Eng., Boston University, hanieh@bu.edu.
Hanieh
H
Mirzaei
D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, {midas, dbeglov, vajda}@bu.edu.
Dima
D
Kozakov
D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, {midas, dbeglov, vajda}@bu.edu.
Dmitri
D
Beglov
Dept. of Electrical & Computer Eng., and Division of Systems Eng., Boston University, yannisp@bu.edu.
Ioannis Ch
IC
Paschalidis
D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, {midas, dbeglov, vajda}@bu.edu.
Sandor
S
Vajda
Division of Systems Eng., Boston University, hanieh@bu.edu.
Pirooz
P
Vakili