Docking functions

Verbosity 2 Num. Answers 50 Output Format SYBYL Database v Multi-mol2 Create Answer Tables Docking Function FlexX v Drug Score Default canfig.dat IX/ tables/defaul t. dat... 

Ubichinone oxidases do not contain CuA-dimers, although they may be restored by site-directed mutagenesis of a few amino acids [278 a]. This suggests that the CuA-binding site which, in cytochrome c oxidases, accepts electrons from cytochrome c, was lost. The docking -function for cytochrome c was no longer required as ubichinone is the physiological electron-donor. 

Perez C, Ortiz AR. Evaluation of docking functions for protein-ligand docking. J Med Chem 2001 44 3768-3785. 

Are there other roles for the basal lamina during regeneration Once axons are guided to the muscle basal lamina by Schwann cell columns, adhesive molecules in the muscle basal lamina may play a docking function to help stabilize synapses. Existing end-plates, thereby, may be better able than other surfaces of muscle to retain contacts with... 

There are still many unsolved problems in computational chemistry and, as discussed, many of them are not new. We still need a method for the quick and accurate calculation of free energies, and we need to understand the limits on the accuracy of any predictive methods. More broadly, what confidence limits can we put on any given prediction from any given level of theory For virtual screening, what are the most important terms left out of the standard docking functions, and indeed higher simulation methods Can we imagine a set of widely accepted well-validated model systems and benchmarks, both for experiment and theory ... 

The cross relation has proven valuable to estimate ET rates of interest from data tliat might be more readily available for individual reaction partners. Simple application of tire cross-relation is, of course, limited if tire electronic coupling interactions associated with tire self exchange processes are drastically different from tliose for tire cross reaction. This is a particular concern in protein/protein ET reactions where tire coupling may vary drastically as a function of docking geometry. 

The calculation of the binding affinity with con.sidcration of all tbc.se effects for virtual screening is not possible. In order to circumvent thus difficulty, scoring functions arc used instead, c.g., the Liidi scoring function [80, or consensus scoring functions derived from FlevX score, DOCK score, GOLD score, ChemScore, or PMF score [81 ]. 

Genetic algorithms can also be used to perform molecular docking [Judson et d. 1994 Jont et d. 1995b Oshiro et d. 1995]. Each chromosome codes not only for the internal conform tion of the ligand as described in Section 9.9.1 but also for the orientation of the ligand withi the receptor site. Both the orientation and the internal conformation will thus vary as th populations evolve. The score of each docked structure within the site acts as the fitnes function used to select the individuals for the next iteration. 

Fig. 12.23 Two simple scoring functions used in docking. On the left is the basic scoring scheme used by the DOCK program [Desjarlais et al. 1988], On the right is the piecewise linear potential [Cclhaar et al. 1995],...

A, C W Murray, D E Clark, D R Westhead and M D Eldridge 1998. Flexible Docking using Tabu rch and an Empirical Estimate of Binding Affinity. Proteins Structure, Function and Genetics 167-382. 

D S and A J Olson 1990 Automated Docking of Substrates to Proteins by Simulated ealing. Proteins Structure, Function and Genetics 8 195-202. 

Kramer B, M Rarey and T Lengauer 1999. Evaluation of the FLEXX Incremental Constructioi Algorithm for Protein-Ligand Docking. Proteins Structure, Function and Genetics 37 228-241. 

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