Biblio
Direct measurement of the dielectric polarization properties of DNA.,
, Proc Natl Acad Sci U S A, 2014 Sep 2, Volume 111, p.E3624-30, (2014)
Differential stability of 2’F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.,
, Nucleic Acids Res, 2010 Apr, Volume 38, p.2498-511, (2010)
Determining promoter location based on DNA structure first-principles calculations.,
, Genome Biol, 2007, Volume 8, p.R263, (2007)
Destabilization of quadruplex DNA by 8-aminoguanine.,
, Chembiochem, 2006 Jan, Volume 7, p.46-8, (2006)
Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease.,
, J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.,
, PLoS Comput Biol, 2012, Volume 8, p.e1002647, (2012)
Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease,
, Cell, 05/2019, Volume 177, Issue 4, p.881 - 895.e17, (2019)
Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily.,
, Structure, 2010 Mar 10, Volume 18, p.402-14, (2010)
Data mining of molecular dynamics trajectories of nucleic acids.,
, J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)
Correlated motions are a fundamental property of B-sheets,
, Nat Commun, 10/2014, Volume 5, (2014)
Cooperativity in Drug-DNA Recognition: A Molecular Dynamics Study,
, Journal of the American Chemical Society, 2001/12/01, Volume 123, Issue 50, p.12658 - 12663, (2001)
Continuum and discrete calculation of fractional contributions to solvation free energy.,
, J Comput Chem, 2003 Oct, Volume 24, p.1610-23, (2003)
Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field,
, Journal of Chemical Theory and Computation, 2013/01/08, Volume 9, Issue 1, p.119 - 125, (2012)
A consensus view of protein dynamics.,
, Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)
Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer.,
, Nucleic Acids Res, 2009 Sep, Volume 37, p.5589-601, (2009)
The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator.,
, The Journal of Physical Chemistry B, 2013/00/15, (2013)
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.,
, Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)
Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.,
, Nat Biotechnol, 2014 Nov, Volume 32, p.1106-12, (2014)
Comparison of molecular dynamics and superfamily spaces of protein domain deformation.,
, BMC Struct Biol, 2009, Volume 9, p.6, (2009)
Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry,
, ACS Central Science, 05/2017, Volume 3, Issue 5, p.454 - 461, (2017)
COCO: a simple tool to enrich the representation of conformational variability in NMR structures.,
, Proteins, 2009 Apr, Volume 75, p.206-16, (2009)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.,
, Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)
Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.,
, Proteins, 2001 Dec 1, Volume 45, p.428-37, (2001)
Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study,
, Journal of the American Chemical Society, 2015/08/19, Volume 137, Issue 32, p.10205 - 10215, (2015)
Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms.,
, Proteins, 2012 Aug, Volume 80, p.2235-49, (2012)
Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties.,
, J Mol Biol, 2002 Jan 25, Volume 315, p.771-86, (2002)
Characterization of compensated mutations in terms of structural and physico-chemical properties.,
, J Mol Biol, 2007 Jan 5, Volume 365, p.249-56, (2007)
Chapter 7 Molecular Modelling of Nucleic Acids,
, Computational Tools for Chemical Biology, p.165 - 197, (2017)
Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations,
, eLife, 04/2017, Volume 6, p.e22175, (2017)
Challenges and guidelines toward 4D nucleome data and model standards,
, Nature Genetics, 10/2018, Volume 50, Issue 10, p.1352 - 1358, (2018)
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors.,
, FASEB J, 2013 Mar, Volume 27, p.1048-61, (2013)
Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH,
, Angewandte Chemie International Edition, Volume 54, p.10488–10491, (2015)
Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.,
, Org Lett, 2007 Oct 25, Volume 9, p.4503-6, (2007)
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.,
, Nucleic Acids Res, 2016 Jan 4, Volume 44, Issue D1, p.D272-8, (2016)
Benzoderivatives of nucleic acid bases as modified DNA building blocks.,
, J Phys Chem A, 2006 Jan 19, Volume 110, p.510-8, (2006)
Backbone FC-H···O hydrogen bonds in 2’F-substituted nucleic acids.,
, Angew Chem Int Ed Engl, 2013 Nov 11, Volume 52, p.12065-8, (2013)
An atomistic view to the gas phase proteome.,
, Structure, 2009 Jan 14, Volume 17, p.88-95, (2009)
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)
Approaching Elastic Network Models to Molecular Dynamics Flexibility,
, Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)
Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design,
, Journal of Chemical Theory and Computation, 2012/00/10, Volume 8, p.2204 - 2214, (2012)
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives.,
, J Am Chem Soc, 2003 Dec 24, Volume 125, p.16127-38, (2003)
Alternative splicing of transcription factors’ genes: beyond the increase of proteome diversity.,
, Comp Funct Genomics, 2009, p.905894, (2009)
Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species.,
, J Mol Biol, 2004 Jan 9, Volume 335, p.495-502, (2004)
Allosterism and signal transfer in DNA,
, Nucleic Acids Research, 2018/09/06, Volume 46, Issue 15, p.7554 - 7565, (2018)
Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine.,
, J Phys Chem B, 2009 Oct 29, Volume 113, p.14465-72, (2009)
Ab initio study of naphtho-homologated DNA bases.,
, J Phys Chem B, 2008 Feb 21, Volume 112, p.2179-86, (2008)
8-Amino guanine accelerates tetramolecular G-quadruplex formation.,
, Chem Commun (Camb), 2008 Jul 7, p.2926-8, (2008)