Biblio
A DNA methylation map of human cancer at single base-pair resolution,
, Oncogene, 06/2017, p.1-10, (2017)
DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p,
, Nucleic Acids Research, 11/2016, (2016)
The DNA-forming properties of 6-selenoguanine,
, Phys. Chem. Chem. Phys., Volume 16, p.1101-1110, (2014)
DNAlive: a tool for the physical analysis of DNA at the genomic scale.,
, Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)
DNA-triplex stabilizing properties of 8-aminoguanine,
, Nucleic Acids Research, Volume 28, p.4531-4539, (2000)
Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.,
, J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)
The dynamic view of proteins: comment on "Comparing proteins to their internal dynamics: exploring structure-function relationships beyond static structural alignments".,
, Phys Life Rev, 2013 Mar, Volume 10, p.29-30; discussion 39-40, (2013)
Dynamics of B-DNA on the microsecond time scale.,
, J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)
The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine,
, Nucleic Acids Research, Volume 29, p.2522-2534, (2001)
Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct.,
, J Biol Chem, 2004 Jun 4, Volume 279, p.24552-60, (2004)
Effects of local electric fields on the redox free energy of single stranded DNA.,
, Chem Commun (Camb), 2011 Mar 7, Volume 47, p.2646-8, (2011)
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations,
, Journal of Chemical Theory and Computation, Volume 9, p.1222-1229, (2013)
Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells,
, Chemical Communications, 03/2017, Volume 53, Issue 19, p.2870 - 2873, (2017)
Electrostatic component of solvation: comparison of SCRF continuum models.,
, J Comput Chem, 2003 Feb, Volume 24, p.284-97, (2003)
Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations.,
, J Comput Chem, 2003 Jul 30, Volume 24, p.1263-75, (2003)
Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer,
, Genome Biology, 01/2016, Volume 17, p.11, (2016)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
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)
Evidence for transcript networks composed of chimeric RNAs in human cells.,
, PLoS One, 2012, Volume 7, p.e28213, (2012)
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)
Exploration of conformational transition pathways from coarse-grained simulations.,
, Bioinformatics, 2013 Aug 15, Volume 29, p.1980-6, (2013)
Exploring early stages of the chemical unfolding of proteins at the proteome scale.,
, PLoS Computational Biology, 2013/00/01, Volume 9, p.e1003393, (2013)
Exploring polymorphisms in B-DNA helical conformations.,
, Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)
Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity.,
, J Med Chem, 2004 Sep 23, Volume 47, p.4865-74, (2004)
Exploring the Complete Mutational Space of the LDL receptor LA5 Domain Using Molecular Dynamics: Linking SNPs with Disease Phenotypes in Familial Hypercholesterolemia,
, Human Molecular Genetics, (2016)
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?,
, Biophys J, 2004 Aug, Volume 87, p.800-11, (2004)
Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution.,
, Chemistry, 2007, Volume 13, p.1108-16, (2007)
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.,
, BMC Genomics, 2006, Volume 7, p.63, (2006)
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.,
, Biophys J, 2008 Sep, Volume 95, p.2127-38, (2008)
Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian.,
, J Comput Chem, 2008 Mar, Volume 29, p.578-87, (2008)
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study.,
, J Comput Aided Mol Des, 2002 Aug-Sep, Volume 16, p.569-83, (2002)
A fast method for the determination of fractional contributions to solvation in proteins.,
, Protein Sci, 2006 Nov, Volume 15, p.2525-33, (2006)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
FlexServ: an integrated tool for the analysis of protein flexibility.,
, Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.,
, J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Functional and structural conservation of CBS domains from CLC chloride channels.,
, J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)
Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides.,
, Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)
Fuzziness and noise in nucleosomal architecture.,
, Nucleic Acids Res, 2014 Apr, Volume 42, p.4934-46, (2014)
A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins.,
, FEBS Lett, 2010 Jan 21, Volume 584, p.460-6, (2010)
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)
Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct.,
, Pediatr Res, 2000 Sep, Volume 48, p.315-22, (2000)
G-quadruplexes can maintain their structure in the gas phase.,
, J Am Chem Soc, 2006 Mar 22, Volume 128, p.3608-19, (2006)
GRID-MD-A tool for massive simulation of protein channels.,
, Proteins, 2008 Feb 15, Volume 70, p.892-9, (2008)
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.,
, Genome Biol, 2012, Volume 13, p.R106, (2012)
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.,
, J Am Chem Soc, 2002 Mar 27, Volume 124, p.3133-42, (2002)
How accurate are accurate force-fields for B-DNA?,
, Nucleic Acids Research, 01/2017, Volume 45, Issue 7, p.4217-4230, (2017)
How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition,
, Journal of Molecular Biology, 07/2019, (2019)
Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient.,
, J Comput Aided Mol Des, 2005 Jun, Volume 19, p.401-19, (2005)
A hydrophobic similarity analysis of solvation effects on nucleic acid bases.,
, J Mol Model, 2007 Feb, Volume 13, p.357-65, (2007)