Molecular dynamics simulations of small peptides: dependence on dielectric model and pH
V Daggett, PA Kollman, ID Kuntz - … : Original Research on …, 1991 - Wiley Online Library
There has been much interest recently in the structure of small peptides in solution. A recent
study by Bradley and co‐workers [(1989) in Techniques of Protein Chemistry, Hugli, TE, Ed …
study by Bradley and co‐workers [(1989) in Techniques of Protein Chemistry, Hugli, TE, Ed …
Model simulations of DNA dynamics
F Zhang, MA Collins - Physical Review E, 1995 - APS
A simple physical model is developed to study some characteristics of DNA dynamics. The
model uses only a few degrees of freedom so that DNA dynamics can be simulated over …
model uses only a few degrees of freedom so that DNA dynamics can be simulated over …
Distance‐dependent dielectric constants and their application to double‐helical DNA
J Mazur, RL Jernigan - Biopolymers: Original Research on …, 1991 - Wiley Online Library
Detailed studies of structures of biological macromolecules, even in simplified models,
involve many costly and time‐consuming calculations. Any thorough methods require …
involve many costly and time‐consuming calculations. Any thorough methods require …
Toxicity and repair of DNA adducts produced by the natural product yatakemycin
Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial
and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin …
and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin …
Role of base flipping in specific recognition of damaged DNA by repair enzymes
M Fuxreiter, N Luo, P Jedlovszky, I Simon… - Journal of molecular …, 2002 - Elsevier
DNA repair enzymes induce base flipping in the process of damage recognition.
Endonuclease V initiates the repair of cis, syn thymine dimers (TD) produced in DNA by UV …
Endonuclease V initiates the repair of cis, syn thymine dimers (TD) produced in DNA by UV …
Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches
Damaged or mismatched DNA bases result in the formation of physical defects in double-
stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain …
stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain …
Anatomy of highly expressing chromosomal sites targeted by retroviral vectors
C Mielke, K Maass, M Tümmler, J Bode - Biochemistry, 1996 - ACS Publications
The eukaryotic genome contains chromosomal loci with a high transcription-promoting
potential. For their identification in cultured cells, transfer of a reporter gene has to be …
potential. For their identification in cultured cells, transfer of a reporter gene has to be …
The Trapping of a Spontaneously “Flipped-Out” Base from Double Helical Nucleic Acids by Host− Guest Complexation with β-Cyclodextrin: The Intrinsic Base-Flipping …
MA Spies, RL Schowen - Journal of the American Chemical …, 2002 - ACS Publications
β-Cyclodextrin, which forms stable host− guest complexes with purine bases, induces the
melting of RNA and DNA duplexes below their normal melting temperatures. α-Cyclodextrin …
melting of RNA and DNA duplexes below their normal melting temperatures. α-Cyclodextrin …
DNA flexibility variation may dominate DNase I cleavage.
ME Hogan, MW Roberson… - Proceedings of the …, 1989 - National Acad Sciences
In a previous experimental study, we proposed that the bending and torsional stiffness of
DNA display a systematic sequence dependence. Subsequently, we developed an elastic …
DNA display a systematic sequence dependence. Subsequently, we developed an elastic …
Distance and exposure dependent effective dielectric function
B Mallik, A Masunov, T Lazaridis - Journal of Computational …, 2002 - Wiley Online Library
In an effort to develop a dielectric screening function for molecular dynamics simulations of
biomolecules in implicit solvent, effective dielectric constants (Deff) for a large number of …
biomolecules in implicit solvent, effective dielectric constants (Deff) for a large number of …