… Desmond, a software package for commodity clusters developed at DE Shaw Research,
allowed simulations nearly an order of magnitude faster than previously possible on the same …

… A recent study by Hub and de Groot also used extensive MD in combination with umbrella
… Moraes, and other members of DE Shaw Research for suggestions and critical comments. …

… Author links open overlay panel Stefano Piana 1 , John L Klepeis 1 , David E Shaw 1 2 …
De novo prediction of protein folding pathways and structure using the principle of sequential …

An outstanding challenge in the field of molecular biology has been to understand the
process by which proteins fold into their characteristic three-dimensional structures. Here, we …

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic
level of detail, but they have been limited to time scales shorter than those of many …

Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor,
Glide approximates a complete systematic search of the conformational, orientational, and …

Recent advances in hardware and software have enabled increasingly long molecular
dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the …

Although molecular dynamics (MD) simulations of biomolecular systems often run for days
to months, many events of great scientific interest and pharmaceutical relevance occur on …

Rationale: Heterogeneity in asthma expression is multidimensional, including variability in
clinical, physiologic, and pathologic parameters. Classification requires consideration of …

The application of all‐atom force fields (and explicit or implicit solvent models) to protein
homology‐modeling tasks such as side‐chain and loop prediction remains challenging both …