Robert E. Duke
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View article: Recent Developments in Amber Biomolecular Simulations
Recent Developments in Amber Biomolecular Simulations Open
Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA…
View article: Recent Estimates of the Structure of the Factor VIIa (FVIIa)/Tissue Factor (TF) and Factor Xa (FXa) Ternary Complex
Recent Estimates of the Structure of the Factor VIIa (FVIIa)/Tissue Factor (TF) and Factor Xa (FXa) Ternary Complex Open
The putative structure of the Tissue Factor/Factor VIIa/Factor Xa (TF/FVIIa/FXa) ternary complex is reconsidered. Two independently derived docking models proposed in 2003 (one for our laboratory: CHeA and one from the Scripps laboratory: …
View article: Computational study of the putative active form of protein Z (PZa): Sequence design and structural modeling
Computational study of the putative active form of protein Z (PZa): Sequence design and structural modeling Open
Although protein Z (PZ) has a domain arrangement similar to the essential coagulation proteins FVII, FIX, FX, and protein C, its serine protease (SP)-like domain is incomplete and does not exhibit proteolytic activity. We have generated a …
View article: Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility
Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility Open
We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed …
View article: Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential Open
We have calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the liga…
View article: A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa)
A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa) Open
Protein Z-dependent protease inhibitor (ZPI) and antithrombin III (AT3) are members of the serpin superfamily of protease inhibitors that inhibit factor Xa (FXa) and other proteases in the coagulation pathway. While experimental structural…
View article: Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*
Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM* Open
Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based G…
View article: Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*
Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM* Open
Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based G…
View article: Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*
Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM* Open
Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based G…
View article: Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*
Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM* Open
Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based G…