D
David A. Case
Researcher at Rutgers University
Publications - 369
Citations - 84216
David A. Case is an academic researcher from Rutgers University. The author has contributed to research in topics: Molecular dynamics & Solvation. The author has an hindex of 102, co-authored 364 publications receiving 74066 citations. Previous affiliations of David A. Case include University of Utah & Scripps Health.
Papers
More filters
Journal ArticleDOI
RNAMotif, an RNA secondary structure definition and search algorithm
Thomas J. Macke,David J. Ecker,Robin R. Gutell,Daniel Gautheret,David A. Case,Rangarajan Sampath +5 more
TL;DR: A new computational motif search algorithm that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements is described and its utility is demonstrated.
Journal ArticleDOI
Constant pH molecular dynamics in generalized Born implicit solvent.
TL;DR: A new method is proposed for constant pH molecular dynamics (MD), employing generalized Born (GB) electrostatics, and a strong correlation between conformation and protonation state is noted and quantitatively analyzed, emphasizing the importance of sampling protonated states in conjunction with dynamics.
Journal ArticleDOI
Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model
Vickie Tsui and,David A. Case +1 more
TL;DR: In this paper, a generalized Born (GB) model was applied to molecular dynamics simulations of the A and B-forms of a duplex DNA d(CCAACGTTGG)2 and the corresponding duplex RNA r(CCACGUUGG)2, resulting in good agreement with simulations using explicit water solvent in terms of both structure and energetics.
Journal ArticleDOI
Effective Born radii in the generalized Born approximation: the importance of being perfect.
TL;DR: The results quantify the importance of getting the effective Born radii right; indeed, with perfect radii, the GB model gives a very good approximation to the underlying PE theory for a variety of biomacromolecular types and conformations.