Alchemical FEP Calculations of Ligand Conformer Focusing in Explicit Solvent

• Published in: Journal of chemical theory and computation Vol. 9; no. 2; pp. 1093 - 1102
• Main Authors: Zeifman, Alexey A, Stroylov, Victor V, Novikov, Fedor N, Stroganov, Oleg V, Kulkov, Val, Chilov, Ghermes G
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 12.02.2013

Slow rotational degrees of freedom in ligands can make alchemical FEP simulations unreliable due to inadequate sampling. We addressed this problem by introducing a FEP-based protocol of ligand conformer focusing in explicit solvent. Our method involves FEP transformations between conformers using eq...