. Author manuscript; available in PMC: 2013 Nov 7.

Published in final edited form as: Curr Pharm Des. 2012;18(9):1217–1239. doi: 10.2174/138161212799436386

Table 1.

Major methods for flexible active site modeling

Methods	Level of flexibility	Algorithm optimization	Reference
oft potentials	Side-chain	Toleration of minor steric clashes	[79–82]
Rotamer libraries random sampling	Side-chain, backbone	Discrete rotamer libraries, Monte Carlo minimization	[80, 81, 83–85, 99]
MD ensemble sampling	Side-chain, backbone, domain	Normal mode (low mode), temperature replica exchange	[88–90, 93]
4D docking	Side-chain, backbone	Flexibility as the 4^th discrete dimension of docking grids	[96]
QSiCR	Side-chain, backbone	Knowledge-based machine learning	[97, 98]