Addressing Two Issues on Conformational Differences and Utility of Random Number Generators in Conformational Sampling

Conformation search procedure is carried out to generate an ensemble of conformations that could be used for purposes such as to address the problem of ligand and receptor flexibility during molecular docking, protein structure predictions, loop modeling and to calculate binding properties. Two important aspects have been discussed, the criteria of different conformations for the purpose of effective conformation sampling in systematic conformation searches, and the redundancies of using random number generators in random searches.