Generalized Born radii computation using linear models and neural networks
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz818
Abstract: MOTIVATION Implicit solvent models play an important role in describing the thermodynamics and the dynamics of biomolecular systems. Key to an efficient use of these models is the computation of Generalized Born (GB) radii, which… read more here.
Keywords: generalized born; computation; born radii; radii ... See more keywords
On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome
Sign Up to like & getrecommendations! Published in 2017 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2017.00003
Abstract: Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with… read more here.
Keywords: generalized born; born solvent; propensity generalized; dark proteome ... See more keywords
The Intrinsic Radius as a Key Parameter in the Generalized Born Model to Adjust Protein-Protein Electrostatic Interaction
Sign Up to like & getrecommendations! Published in 2023 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms24054700
Abstract: The generalized Born (GB) model is an extension of the continuum dielectric theory of Born solvation energy and is a powerful method for accelerating the molecular dynamic (MD) simulations of charged biological molecules in water.… read more here.
Keywords: energy; generalized born; born model; model ... See more keywords