Biblio
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)
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)
The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator.,
, The Journal of Physical Chemistry B, 2013/00/15, (2013)
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)
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations,
, Journal of Chemical Theory and Computation, Volume 9, p.1222-1229, (2013)
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)
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)
Improved nucleic acid descriptors for siRNA efficacy prediction.,
, Nucleic Acids Res, 2013 Feb 1, Volume 41, p.1383-94, (2013)
Light on the structural communication in Ras GTPases.,
, J Biomol Struct Dyn, 2013, Volume 31, p.142-57, (2013)
NAFlex: a web server for the study of nucleic acid flexibility.,
, Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
On the nature of DNA hyperchromic effect.,
, J Phys Chem B, 2013 Jul 25, Volume 117, p.8697-704, (2013)
Proteins in the gas phase,
, WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.,
, J Chem Theory Comput, 2013, Volume 9, p.707-721, (2013)
Toward an atomistic description of the urea-denatured state of proteins.,
, Proc Natl Acad Sci U S A, 2013 Apr 9, Volume 110, p.5933-8, (2013)
Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations,
, PLoS Comput Biol, 11, Volume 9, p.e1003354, (2013)
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.,
, Nucleic Acids Res, 2013 Aug, Volume 41, p.7220-30, (2013)
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)
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)
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)
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.,
, PLoS Comput Biol, 2012, Volume 8, p.e1002647, (2012)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
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)
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)
Exploring polymorphisms in B-DNA helical conformations.,
, Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.,
, Genome Biol, 2012, Volume 13, p.R106, (2012)
Impact of methylation on the physical properties of DNA.,
, Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.,
, Bioinformatics, 2012 May 1, Volume 28, p.1278-9, (2012)
Structure of triplex DNA in the gas phase.,
, J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.,
, Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.,
, Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)
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)
Molecular basis of substrate-induced permeation by an amino acid antiporter.,
, Proc Natl Acad Sci U S A, 2011 Mar 8, Volume 108, p.3935-40, (2011)
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding.,
, J Am Chem Soc, 2011 Aug 10, Volume 133, p.12154-61, (2011)
Nucleotide binding switches the information flow in ras GTPases.,
, PLoS Comput Biol, 2011 Mar, Volume 7, p.e1001098, (2011)
nucleR: a package for non-parametric nucleosome positioning.,
, Bioinformatics, 2011 Aug 1, Volume 27, p.2149-50, (2011)
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)
Polarization effects in molecular interactions,
, WIREs Comput Mol Sci, 2011, Volume 1, p.844 - 854, (2011)
The protein folding transition-state ensemble from a Go-like model.,
, Phys Chem Chem Phys, 2011 Sep 7, Volume 13, p.15166-74, (2011)
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking.,
, J Chem Inf Model, 2011 Feb 28, Volume 51, p.370-7, (2011)
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering.,
, J Mol Biol, 2011 Mar 4, Volume 406, p.604-19, (2011)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.,
, J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.,
, J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks.,
, Structure, 2011 Jun 8, Volume 19, p.881-9, (2011)
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.,
, Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)