GPU-accelerated molecular modeling coming of age

GPU Accelerated Molecular Surface Computing

A method is presented for computing the SES (solvent excluded surface) of a protein molecule in interactive-time based on GPU (graphics processing unit) acceleration. First, the offset surface of the van der Waals spheres is sampled using an offset distance d that corresponds to the radius of the solvent probe. The SES is then constructed by extracting the surface at distance d from the sample ...

Molecular diagnostics of lymphoma: coming of age.

Molecular diagnostics of ADPKD coming of age.

E ver since the first autosomal dominant polycystic kidney disease (ADPKD) gene was localized to a chromosomal interval (PKD1: 16p13.3) in 1985, brave souls have been performing molecular-based diagnostics (1). The enthusiasm was tempered by the discovery of a second gene (PKD2: 4q21) and suggestions of a third, with the realization that reliable linkage-based diagnostics required families larg...

GPU-Accelerated Computation and Interactive Display of Molecular Orbitals

In this chapter, we present several GPU algorithms for evaluating molecular orbitals on three-dimensional lattices, as is commonly used for molecular visualization. For each kernel, we describe necessary design trade-offs, applicability to various problem sizes, and performance on different generations of GPU hardware. Further, we demonstrate the appropriate and effective use of fast on-chip GP...

Coming of age: molecular drivers of aging and therapeutic opportunities.

Aging is like the weather: everyone talks about it, but no one seems to do anything about it. We believe this may soon change, as an improved understanding of the molecular and genetic pathways underlying aging suggests it is possible to therapeutically target the aging process and increase health span. This Review series focuses on fundamental cellular mechanisms of aging and their relationshi...