Modelling Protein–Protein and Protein–DNA Docking

The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking

“…8,[30][31][32][33] The initial global shape complementarity search was carried out with a grid spacing of 0.7 Å and an angle step size of 98. Twentyseven thousand possible dockings were kept from this stage, and then reranked with a scoring function (RPScore) derived from the statistics of residue-residue contacts in a database of 92 non-redundant complexes.…”

“…This uses surface-complementarity-based scoring in a rigid body search, 30,31 followed by rescoring 32,33 and an optional final side-chain refinement 8 (not used here). Although sometimes, in some regions, the MD simulations do approach closer to the bound conformations, it was necessary to confirm their usefulness directly, since there is not a clear correlation between the size of the conformational change on docking and the difficulty of predicting the complex.…”

“…8,[30][31][32][33] To summarize, the program exhaustively searches the space of relative translations and rotations of receptor and ligand, keeping several thousand candidate complexes based on high surface complementarity and a negative electrostatic energy. These are then re-assessed using a scoring function called RPScore, derived from the statistics of residue-residue contacts in the PDB, and clustered.…”

Crystal Structure of the Phosphoenolpyruvate-binding Enzyme I-Domain from the Thermoanaerobacter tengcongensis PEP: Sugar Phosphotransferase System (PTS)

“…Three-dimensional structures of E-ClPEP and Z-ClPEP were created using the Dundee PRODRG2 server, 58 and were superimposed on P-pyr, an inhibitor of pyruvate phosphate dikinase 25 using O. Molecular modeling was performed with the program 3D-Dock. 59,60 Structure Figures were created using the program PYMOL (www.pymol.org).…”

Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration

“…Random sampling methods were also developed in [2, 24, 27, 34]. Problems of sampling rotational groups and spheres have been studied and applied in the context of computational structural biology, physics, chemistry, computer graphics and robotics [4, 7, 16, 19, 21, 26, 30, 31, 32]. …”