Grid-search molecular accessible surface algorithm for solving the protein docking problem
Journal of Computational Chemistry
Molecular docking using shape descriptors
Journal of Computational Chemistry
New contact measures for the protein docking problem
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Spherical Harmonic Molecular Surfaces
IEEE Computer Graphics and Applications
Efficient Unbound Docking of Rigid Molecules
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
3-D Docking of Protein Molecules
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes
VIS '04 Proceedings of the conference on Visualization '04
SIAM Journal on Scientific Computing
SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The functions of proteins are often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination, and understanding function and structure relationships. In this paper, we extend our nonuniform fast Fourier transform-based docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code {\rm F}^2Dock (F^2= {\rm \underline{F}ast\underline{F}ourier}). We have calibrated {\rm F}^2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that {\rm F}^2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, {\rm F}^2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .