Peptide docking

Totrov, M. Accurate and efficient generalized Bom model based on solvent accessibility derivation and application for logP octanol/water prediction and flexible peptide docking, f Comput. Chem. 2004, 25, 609-619. 

In the preferential interaction model, the equilibrium association constant, K.ISVIC, for a peptide docked to a RPC sorbent can be related via eq 6 to the changes in the preferential interaction of the solvent and water with the peptide P- the ligands L, and the peptide-ligand complex PtL as a function of solvent concentration, [3]m. The effect of preferential hydration/solvation of a peptide on k can be represented in terms of the following expression t85l... 

It is, however, pertinent to state here that this type of suggestive action mode is proved to be quite good and effective for peptide docking, but it may turn out to be farily expensive proposition. Therefore, it is always advisible and wise to prescreen the proposed ligand flexibility in particular. 

Floudas, C. A., Klepeis, J. L., and Pardalos, P. M. 1999. Global optimization approaches in protein folding and peptide docking. In DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Eds. Farach-Colton M., Roberts, F. S., Vingron, M., and Waterman, M., American Mathematical Society, 47 141-171. 

TrelletM, MelquiondA, Bonvin A (2013) Aunified conformational selection and induced fit approach to protein-peptide docking. PLoS One 8 e58769... 

Understanding protein-protein interactions, also known as peptide docking, is critically important for rational protein engineering and pharmaceutical design. 

A recent review of approaches for peptide docking can be found in Floudas et al. [235]. The main disadvantages of most of these approaches are as follows ... 

Thus many current models of binding site stmcture prediction and binding affinity prediction in peptide docking are not able to guarantee that they have found the optimum docking solution because they consider only a few of the many conformations two docking partners may adopt, because they are not quantitative, or because they do not fully consider enfropic, electrostatic, or other energetic effects. 

Figure 57. Schematic diagram for peptide docking global optimization. The arrows indicate the direction of information flow. The names of input, output, and source code files are indicated. References to / / and / only describe whether gradient evaluations or only function evaluations are used.

The intense worldwide experimental and theoretical research effort directed toward solving the protein folding and peptide docking problems underscores their importance. The ability to predict computationally the folding of proteins and the formation of protein-protein complexes would support and help direct experimental work in biology, chemistry, biophysics, and pharmaceutical development. In this review we have shown that molecular modeling and global optimization are the dominant factors that will provide solutions to these problems. 

Floudas CA, Klepeis JL, Pardalos PM (1999) Global optimization approaches in protein folding and peptide docking. American Mathematical Society, New Jersey... 

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