Biblio
] Dynamics of B-DNA on the microsecond time scale.,
, J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)
Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds,
, Journal of medicinal chemistry, Volume 54, Number 12, p.4042–4056, (2011)
The relative flexibility of B-DNA and A-RNA duplexes: database analysis.,
, Nucleic Acids Res, 2004, Volume 32, p.6144-51, (2004)
Towards a molecular dynamics consensus view of B-DNA flexibility.,
, Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)
Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A Quantum Mechanics/Molecular Mechanics Study,
, The Journal of Physical Chemistry Letters, 12/2022, Volume 13, Issue 51, p.12004 - 12010, (2022)
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)
Screening of inhibitors of porcine dipeptidyl peptidase IV activity in aqueous extracts from marine organisms,
, Enzyme Microb. Technol., Volume 40, Number {3, SI}, {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, p.414-419, (2007)
Effect of divalent cations on the porcine kidney cortex membrane-bound form of dipeptidyl peptidase IV.,
, Int J Biochem Cell Biol, 2011 Mar, Volume 43, p.363-71, (2011)
Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair,
, Nature Communications, 08/2023, Volume 14, Issue 1, p.5104, (2023)
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)
A theoretical view of protein dynamics,
, Chem. Soc. Rev., Volume 43, p.5051-5066, (2014)
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems.,
, Chem Rev, 2000 Nov 8, Volume 100, p.4187-4226, (2000)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.,
, Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)
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)
Theoretical methods for the simulation of nucleic acids.,
, Chem Soc Rev, 2003 Nov, Volume 32, p.350-64, (2003)
Recent advances in the study of nucleic acid flexibility by molecular dynamics.,
, Curr Opin Struct Biol, 2008 Apr, Volume 18, p.185-93, (2008)
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community),
, F1000Research, 04/2020, Volume 9, (2020)
Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope,
, Proceedings of the National Academy of Sciences, 04/2019, (2019)
Approaching Elastic Network Models to Molecular Dynamics Flexibility,
, Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations,
, Nat Commun, 2016/08/31, Volume 7, (2016)
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility.,
, J Am Chem Soc, 2008 Mar 19, Volume 130, p.3486-96, (2008)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid.,
, J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)
Relative flexibility of DNA and RNA: a molecular dynamics study.,
, J Mol Biol, 2004 Oct 22, Volume 343, p.627-38, (2004)
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)
Data mining of molecular dynamics trajectories of nucleic acids.,
, J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)
The impact of monovalent ion force field model in nucleic acids simulations.,
, Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (2009)
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)
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution,
, Nat Struct Mol Biol , 10/2022, Volume in press, (2022)
Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria,
, Science, 07/2023, Volume 380, Issue 6651, p.eadh9351, (2023)
The protein folding transition-state ensemble from a Go-like model.,
, Phys Chem Chem Phys, 2011 Sep 7, Volume 13, p.15166-74, (2011)
The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator.,
, The Journal of Physical Chemistry B, 2013/00/15, (2013)
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)
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.,
, Genome Biol, 2012, Volume 13, p.R106, (2012)
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)
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)
Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer’s disease.,
, Curr Pharm Des, 2004, Volume 10, p.3131-40, (2004)
Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index.,
, J Comput Chem, 2002 Apr 15, Volume 23, p.554-63, (2002)
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?,
, Proteins, 2004 Nov 15, Volume 57, p.458-67, (2004)
Continuum and discrete calculation of fractional contributions to solvation free energy.,
, J Comput Chem, 2003 Oct, Volume 24, p.1610-23, (2003)
Partition of protein solvation into group contributions from molecular dynamics simulations.,
, Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)
DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.,
, Nat Biotechnol, 2014 Nov, Volume 32, p.1106-12, (2014)
Visualizing phosphodiester-bond hydrolysis by an endonuclease.,
, Nat Struct Mol Biol, 2015 Jan, Volume 22, p.65-72, (2015)
Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells,
, Nucleic Acids Res, 04/2024, Volume 52, Issue 6, p.3375 - 3389, (2024)
Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH,
, Journal of the American Chemical Society, 11/2017, Volume 139, Issue 40, p.13985 - 13988, (2017)
Proteins in the gas phase,
, WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)
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)
An atomistic view to the gas phase proteome.,
, Structure, 2009 Jan 14, Volume 17, p.88-95, (2009)