Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.

ABSTRACT: The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to

SUBMITTER: Nguyen H 

PROVIDER: S-EPMC4805114 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature