CHARMM: the biomolecular simulation program
BR Brooks, CL Brooks III… - Journal of …, 2009 - Wiley Online Library
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …
widely used molecular simulation program. It has been developed over the last three …
[图书][B] DNA and RNA modification enzymes: structure, mechanism, function and evolution
H Grosjean - 2009 - taylorfrancis.com
This volume is a timely and comprehensive description of the many facets of DNA and RNA
modification-editing processes and to some extent repair mechanisms. Each chapter offers …
modification-editing processes and to some extent repair mechanisms. Each chapter offers …
Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields
E Fadrná, N Špačková, J Sarzynska… - Journal of chemical …, 2009 - ACS Publications
We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two
DNA quadruplex (G-DNA) molecules, namely the antiparallel d (G4T4G4) 2 dimeric …
DNA quadruplex (G-DNA) molecules, namely the antiparallel d (G4T4G4) 2 dimeric …
Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, BI, and BII Forms of Duplex DNA
AD MacKerell, Jr - The Journal of Physical Chemistry B, 2009 - ACS Publications
Canonical forms of duplex DNA are known to sample well-defined regions of the α, β, γ, ε,
and ζ dihedral angles that define the conformation of the phosphodiester linkage in the …
and ζ dihedral angles that define the conformation of the phosphodiester linkage in the …
Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A′-RNA Distinct Conformational Structures?
We use molecular dynamics simulations to compare the conformational structure and
dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A …
dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A …
Molecular Modeling of Base Flipping in DNA
UD Priyakumar, AD MacKerell Jr - DNA and RNA Modification …, 2009 - books.google.com
DNA modification and repairenzymes are capable of rotatinga DNAbase to an extrahelical
state, an event commonly referred to as 'base flipping,* and perform a specific chemical …
state, an event commonly referred to as 'base flipping,* and perform a specific chemical …