D
Daniel R. Roe
Researcher at National Institutes of Health
Publications - 32
Citations - 6436
Daniel R. Roe is an academic researcher from National Institutes of Health. The author has contributed to research in topics: Molecular dynamics & Solvation. The author has an hindex of 19, co-authored 30 publications receiving 4625 citations. Previous affiliations of Daniel R. Roe include Stony Brook University & Rutgers University.
Papers
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Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
TL;DR: PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.
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Improved Generalized Born Solvent Model Parameters for Protein Simulations
TL;DR: The new GB model (GB-Neck2) has better agreement to Poisson-Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins.
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Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Tyler Luchko,Sergey Gusarov,Daniel R. Roe,Carlos Simmerling,David A. Case,Jack A. Tuszynski,Andriy Kovalenko +6 more
TL;DR: The three-dimensional molecular theory of solvation coupled with molecular dynamics simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps to enable simulation of large biomolecules is presented.
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Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
TL;DR: These molecular dynamics simulations suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale.
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Evaluation of DOCK 6 as a pose generation and database enrichment tool
Scott R. Brozell,Sudipto Mukherjee,Trent E. Balius,Daniel R. Roe,David A. Case,Robert C. Rizzo +5 more
TL;DR: Overall, the breadth and number of experiments performed provide a useful snapshot of current capabilities of DOCK6 as well as starting points to guide future development efforts to further improve sampling and scoring.