GRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

ABSTRACT: Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residu

SUBMITTER: Sercinoglu O 

PROVIDER: S-EPMC6030995 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature