3 papers
q-bio.BM2024
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
q-bio.BM2024
Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs
Xin Cao, Michelle H. Hummel, Yuzhang Wang +2
In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (SASA) analytically along with atomic derivatives on G…
cs.CG2017
Laguerre-Intersection Method for Implicit Solvation
Michelle Hatch Hummel, Bihua Yu, Carlos Simmerling +1
Laguerre tessellations of macromolecules capture properties such as molecular interface surfaces, volumes and cavities. Explicit solvent molecular dynamics simulations of a macromo…