Docking by simulation

S. Yue, Protein Eng., 4,177 (1990). Distance-Constrained Molecular Docking by Simulated... 

Motiejunas D, Gabdoulline RR, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins. In Press. 

S. Yue. Distance-constrained molecular docking by simulated annealing. Protein Engineering, 4(2) 177—184, 1990. 

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

DS Goodsell, AJ Olson. Automated docking of substrates to proteins by simulated annealing. Proteins Struct Funct Genet 8 195-202, 1990. 

X-ray crystallography, docking modes can be validated by various NMR techniques NOEs may be observed between the ligand and the receptor protein by heteronuclear-filtered NOE spectroscopy [51], chemical shift changes of protein resonances upon binding can be analyzed by simulation of shifts caused by ring currents and electrostatic effects [52], and saturation transfer difference measurements indicate which part of the ligand is in direct contact with the protein [52]. 

Configurationally biased Monte Carlo techniques [63-65] have made it possible to compute adsorption isotherms for linear and branched hydrocarbons in the micropores of a siliceous zeolite framework. Apart from Monte Carlo techniques, docking techniques [69] have also been implemented in some available computer codes. Docking techniques are convenient techniques that determine, by simulated annealing and subsequent freezing techniques, local energy minima of adsorbed molecules based on Lennard-Jones-or Buckingham-type interaction potentials. 

Wang, T, Wade, R. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 2003, 50,158-69. 

Two recent approaches that differ substantially from earlier docking methods are worth mentioning. In the procedure of Li, Moal, and Bates,a simulation framework is used to search for encounter complexes by simulating collisions between multiple copies of the component proteins in a crowded environment. The frequency of collisions and the retention time (the time interval any two proteins remain in contact during the simulations) are then employed to discriminate between specific and nonspecific complexes, with promising results. 

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