Alexander D. MacKerell Jr..
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of
conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational
Structure-Based Drug Discovery (CSBDD) projects. This paper introduces the reader to the fundamentals of MM, with a special emphasis
on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments
such as polarizable force fields are discussed. The paper ends with a brief overview of common force fields in CSBDD.
Keywords: Molecular mechanics, force fields, structure-based drug design.
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