Docking flexible

Local motions Ligand docking flexibility Femtoseconds (fs) to picosec-... 

Docking flexible ligands to macromolecular receptors by molecular shape, J. Med. 

Dixon, J.S., Kuntz, I.D., and Venkataraghavan, R. Docking flexible ligands to macromolecular receptors by molecular shape./. Med. Chem. 1986,... 

Kramer, B., Rarey, M., Lengauer, T. (1997) CASP2 experiences with docking flexible ligands using FlexX. Proteins Suppl 1, 221-225. 

CASP2 Experiences with Docking Flexible Ligands Using FlexX. 

Chem., 29, 2149 (1986). Docking Flexible Ligands to Macromolecular Receptors by Molecular Shape. 

Conformational Search Method for Docking Flexible Molecules Using Molecular Similarity. 

Judson, R.S. etal. Docking flexible molecules - a case study of three proteins./. Comp. Chem., 1995,16,1405-1419. 

S. Makino and I. D. Kuntz. ELECT++ Faster conformational search method for docking flexible molecules using molecular similarity. Journal of Computational Chemistry, 19 1834-1852, 1998. 

B. Kramer, M. Rarey, and T. Lengauer. Casp-2 experiences with docking flexible ligands using flexx. PROTEINS ... 

Zhao, Y. and Sanner, M.F. (2007) FLIPDock docking flexible ligands into flexible receptors. Proteins, 68, 726-737. 

Figure 8.1 Protein flexibility can be incorporated in several docking stages before, while, or after ligand placement. Preliminary to docking, flexibility analysis identifies flexible parts. The information obtained is used for adequate receptor...

Prodock The program docks flexible hgands to a flexible binding site (representing the structure 16... 

R. S. Judson, E. P. Jaeger, and A. M. Treasurywala, J. Mol. Struct. (THEOCHEM), 308,191 (1994). A Genetic Algorithm-Based Method for Docking Flexible Molecules. 

As discussed above, side-chain movement or protein flexibility plays an important role in a docking process. Usually, uncertainly in side-chain placement or loop modelhng arises in protein stmctures predicted through homology modelling. Only a few docking tools consider these, like FlexE. This is a tool which considers the protein structure variations or flexibility to dock flexible ligands [22] (Fig. 4.51). 

Caflisch et al. demonstrated that a two-step procedure incorporating a Monte Carlo minimization procedure can dock flexible oligopeptides to static proteins. Step one involves rigid rotations and translations of a preselected conformation. Step two involves taking the low energy conformation(s) produced in step one and carrying out 400 cycles of Monte Carlo minimization. The bound conformation of the HIV protease inhibitor MVT-101 was well reproduced by the method. 

We performed molecular modelling studies, to rationalize the NMR experiment results described above. The Dock module of MOE was used to dock flexible FLZ into a rigid P-CD (25 runs). From the resulting complex, the one with the best binding energy was then energy-minimized keeping both FLZ and P-CD... 

Because rigid pharmacophoric searching is based on the positions of explicit atoms or points, it is often difficult to pose queries based on directed vectors in space. A specialized search system, CAVEAT, has been developed that permits the specification of queries based on the relative orientation and position of bond vectors in space. If the query bond vectors have been derived from a docked flexible ligand, then when a database of rigid ring-systems (CAST-3D or CSD) is searched, CAVEAT will identify potential substructural skeletons which could act as a rigid mimic of the core substructure of the ligand. 

---