User profiles for D. Shaw
David E. ShawDE Shaw Research Verified email at deshaw.com Cited by 60002 |
Biomolecular simulation: a computational microscope for molecular biology
… 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 …
allowed simulations nearly an order of magnitude faster than previously possible on the same …
Long-timescale molecular dynamics simulations of protein structure and function
… 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. …
… Moraes, and other members of DE Shaw Research for suggestions and critical comments. …
[HTML][HTML] Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
… 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 …
De novo prediction of protein folding pathways and structure using the principle of sequential …
How fast-folding proteins fold
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 …
process by which proteins fold into their characteristic three-dimensional structures. Here, we …
Atomic-level characterization of the structural dynamics of proteins
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 …
level of detail, but they have been limited to time scales shorter than those of many …
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
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 …
Glide approximates a complete systematic search of the conformational, orientational, and …
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
Recent advances in hardware and software have enabled increasingly long molecular
dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the …
dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the …
Scalable algorithms for molecular dynamics simulations on commodity clusters
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 …
to months, many events of great scientific interest and pharmaceutical relevance occur on …
Cluster analysis and clinical asthma phenotypes
Rationale: Heterogeneity in asthma expression is multidimensional, including variability in
clinical, physiologic, and pathologic parameters. Classification requires consideration of …
clinical, physiologic, and pathologic parameters. Classification requires consideration of …
A hierarchical approach to all‐atom protein loop prediction
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 …
homology‐modeling tasks such as side‐chain and loop prediction remains challenging both …