Biblio
Theoretical methods for the simulation of nucleic acids.,
, Chem Soc Rev, 2003 Nov, Volume 32, p.350-64, (2003)
The relative flexibility of B-DNA and A-RNA duplexes: database analysis.,
, Nucleic Acids Res, 2004, Volume 32, p.6144-51, (2004)
Relative flexibility of DNA and RNA: a molecular dynamics study.,
, J Mol Biol, 2004 Oct 22, Volume 343, p.627-38, (2004)
Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.,
, Chemistry, 2005 Aug 19, Volume 11, p.5062-6, (2005)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid.,
, J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)
Data mining of molecular dynamics trajectories of nucleic acids.,
, J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)
Essential Dynamics: A Tool for Efficient Trajectory Compression and Management,
, Journal of Chemical Theory and Computation, 2006/03/01, Volume 2, Issue 2, p.251 - 258, (2006)
A consensus view of protein dynamics.,
, Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)
Determining promoter location based on DNA structure first-principles calculations.,
, Genome Biol, 2007, Volume 8, p.R263, (2007)
Dynamics of B-DNA on the microsecond time scale.,
, J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.,
, Biophys J, 2007 Jun 1, Volume 92, p.3817-29, (2007)
Theoretical study of large conformational transitions in DNA: the B<–>A conformational change in water and ethanol/water.,
, Nucleic Acids Res, 2007, Volume 35, p.3330-8, (2007)
8-Amino guanine accelerates tetramolecular G-quadruplex formation.,
, Chem Commun (Camb), 2008 Jul 7, p.2926-8, (2008)
DNAlive: a tool for the physical analysis of DNA at the genomic scale.,
, Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.,
, J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)
Recent advances in the study of nucleic acid flexibility by molecular dynamics.,
, Curr Opin Struct Biol, 2008 Apr, Volume 18, p.185-93, (2008)
Towards a molecular dynamics consensus view of B-DNA flexibility.,
, Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.,
, Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
Real-time atomistic description of DNA unfolding.,
, Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.,
, Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)
Toward a consensus view of duplex RNA flexibility.,
, Biophys J, 2010 Sep 22, Volume 99, p.1876-85, (2010)
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast.,
, BMC Genomics, 2011, Volume 12, p.489, (2011)
Exploring polymorphisms in B-DNA helical conformations.,
, Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Impact of methylation on the physical properties of DNA.,
, Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)
Exploring early stages of the chemical unfolding of proteins at the proteome scale.,
, PLoS Computational Biology, 2013/00/01, Volume 9, p.e1003393, (2013)
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.,
, J Chem Theory Comput, 2013, Volume 9, p.707-721, (2013)
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.,
, Nucleic Acids Res, 2014 Oct 29, Volume 42, p.12272-83, (2014)
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
Allosterism and signal transfer in DNA,
, Nucleic Acids Research, 2018/09/06, Volume 46, Issue 15, p.7554 - 7565, (2018)
Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?,
, Biophysical Reviews, 11/2021, (2021)