Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).

ABSTRACT: Gaussian network model (GNM) and anisotropic network model (ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM (gGNM) and ANM methods and show that the GNM Kirchhoff matrix can be built from the ideal low-pass filter, which is a special case of a wide class of correlation functions underpinning the linear scaling flexibility-rigidity index (FRI) method. Based on the mathematical structure of correlation functions, we propose a unified framework to construct generalized Kirchhoff matrices whose matrix inverse leads to gGNMs, whereas, the direct inverse of its diagonal elements gives rise to FRI method. With this connection, we further introduce two multiscale elastic network models, namely, multiscal

SUBMITTER: Xia K 

PROVIDER: S-EPMC4670452 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature