A rapid solvent accessible surface area estimator for coarse grained molecular simulations
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24709
Abstract: The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with… read more here.
Keywords: solvent accessible; surface area; accessible surface; solvent ... See more keywords
Analytical calculation of the solvent‐accessible surface area and its nuclear gradients by stereographic projection: A general approach for molecules, polymers, nanotubes, helices, and surfaces
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26191
Abstract: In this article, we explore an alternative to the analytical Gauss–Bonnet approach for computing the solvent‐accessible surface area (SASA) and its nuclear gradients. These two key quantities are required to evaluate the nonelectrostatic contribution to… read more here.
Keywords: solvent accessible; nuclear gradients; stereographic projection; calculation ... See more keywords
Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of proteomics"
DOI: 10.1016/j.jprot.2020.103793
Abstract: The activity of most proteins and protein complexes relies on the formation of defined three-dimensional structures. The analysis of these arrangements is therefore key for understanding their function and regulation in the cell. Besides the… read more here.
Keywords: accessible amino; acid residues; solvent accessible; amino acid ... See more keywords
Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.
Sign Up to like & getrecommendations! Published in 2024 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.3c01366
Abstract: In this paper, we present differentiable solvent-accessible surface area (dSASA), an exact geometric method to calculate SASA analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to tetrahedra in… read more here.
Keywords: solvent; solvent accessible; surface area; solvent molecular ... See more keywords
An efficient algorithm calculating common solvent accessible volume
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0265614
Abstract: The solvent accessible surface area and the solvent accessible volume are measurements commonly used in implicit solvent models to include the effect of forces exerted by solvents on the protein surfaces (or the atoms on… read more here.
Keywords: solvent accessible; solvent; based method; common solvent ... See more keywords
Application of Hierarchical Clustering to Analyze Solvent-Accessible Surface Area Patterns in Amycolatopsis lipases
Sign Up to like & getrecommendations! Published in 2022 at "Biology"
DOI: 10.3390/biology11050652
Abstract: Simple Summary Solvent-Accessible Surface Area (SASA) as the one dimensional structure property of the protein considers as the measuring the exposure of an amino acid residue to the solvent in one protein. It is an… read more here.
Keywords: amycolatopsis; solvent; solvent accessible; surface area ... See more keywords