User profiles for Brent A. Gregersen
Brent A GregersenDE Shaw Research Verified email at DEShawResearch.com Cited by 4617 |
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 …
Hybrid QM/MM study of thio effects in transphosphorylation reactions
Results of a series of hybrid quantum mechanical/molecular mechanical (QM/MM) activated
dynamics simulations of thio effects in the transphosphorylation (methanolysis) of a 2‘-ribose…
dynamics simulations of thio effects in the transphosphorylation (methanolysis) of a 2‘-ribose…
Mechanism of Na+/H+ Antiporting
…, MP Eastwood, R Flitman-Tene, BA Gregersen…�- Science, 2007 - science.org
Na + /H + antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia
coli NhaA was recently determined, but its mechanisms of transport and pH regulation …
coli NhaA was recently determined, but its mechanisms of transport and pH regulation …
Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation
Transphosphorylation thio effects in solution are studied using hybrid QM/MM calculations
with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed …
with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed …
[HTML][HTML] A common, avoidable source of error in molecular dynamics integrators
…, RO Dror, MP Eastwood, BA Gregersen…�- The Journal of�…, 2007 - pubs.aip.org
In constrained molecular dynamics simulations using some of the most popular molecular
dynamics codes, calculation of the velocities of constrained particles is based solely on the …
dynamics codes, calculation of the velocities of constrained particles is based solely on the …
[HTML][HTML] Quantum chemical benchmark databases of gold-standard dimer interaction energies
Advances in computational chemistry create an ongoing need for larger and higher-quality
datasets that characterize noncovalent molecular interactions. We present three benchmark …
datasets that characterize noncovalent molecular interactions. We present three benchmark …
Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics�…
BA Gregersen, DM York�- The Journal of Physical Chemistry B, 2005 - ACS Publications
New methods for the calculation of electrostatic interactions between the active dynamical
region and surrounding external solvated macromolecular environment in hybrid quantum …
region and surrounding external solvated macromolecular environment in hybrid quantum …
High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods
BA Gregersen, DM York�- The Journal of chemical physics, 2005 - pubs.aip.org
A series of high-order surface element discretization schemes for variational boundary
element methods are introduced. The surface elements are chosen in accord with angular …
element methods are introduced. The surface elements are chosen in accord with angular …
Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory
Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional
methods for the in-line dianionic methanolysis of the native (unsubstituted) and thio-…
methods for the in-line dianionic methanolysis of the native (unsubstituted) and thio-…
A charge‐scaling implementation of the variational electrostatic projection method
BA Gregersen, DM York�- Journal of computational chemistry, 2006 - Wiley Online Library
Two new charge‐scaling methods for efficient modeling of the solvated macromolecular
environment in hybrid QM/MM calculations of biological reactions are presented. The methods …
environment in hybrid QM/MM calculations of biological reactions are presented. The methods …