Biblio
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
Partition of protein solvation into group contributions from molecular dynamics simulations.,
, Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)
On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling".,
, Acc Chem Res, 2009 Apr 21, Volume 42, p.489-92; discussion 493-7, (2009)
Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies.,
, J Phys Chem B, 2009 Jul 9, Volume 113, p.9330-4, (2009)
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies.,
, J Comput Aided Mol Des, 2010 Apr, Volume 24, p.281-91, (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)
Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor,
, Journal of Biological Chemistry, 11/2018, Volume 293, Issue 46, p.17888 - 17905, (2018)
PMUT: a web-based tool for the annotation of pathological mutations on proteins.,
, Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update,
, Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)
Polarization effects in molecular interactions,
, WIREs Comput Mol Sci, 2011, Volume 1, p.844 - 854, (2011)
Predicting the limit of intramolecular H-Bonding with classical molecular dynamics,
, Angewandte Chemie International Edition, 01/2019, (2019)
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations,
, Nat Commun, 2016/08/31, Volume 7, (2016)
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)
A procedure for identifying homologous alternative splicing events.,
, BMC Bioinformatics, 2007, Volume 8, p.260, (2007)
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines.,
, Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)
Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution,
, Biophysical Journal, 05/2018, Volume 114, p.2386 - 2396, (2018)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.,
, Proteins, 2010 Jan, Volume 78, p.83-94, (2010)
The protein folding transition-state ensemble from a Go-like model.,
, Phys Chem Chem Phys, 2011 Sep 7, Volume 13, p.15166-74, (2011)
Proteins in the gas phase,
, WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)
Proton Dynamics in Protein Mass Spectrometry,
, The Journal of Physical Chemistry Letters, 03/2017, Volume 8, Issue 6, p.1105 - 1112, (2017)
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.,
, Nucleic Acids Res, 2005 Jul 1, Volume 33, p.W501-5, (2005)
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data,
, SoftwareX, 12/2016, Volume 5, p.44 - 50, (2016)
Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer,
, Cancer Research, 01/2017, Volume 77, Issue 2, p.459, (2017)
Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression,
, Nucleic Acids Research, 11/2016, Volume 44, p.4354-4367, (2016)
Real-time atomistic description of DNA unfolding.,
, Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)
Recent advances in the study of nucleic acid flexibility by molecular dynamics.,
, Curr Opin Struct Biol, 2008 Apr, Volume 18, p.185-93, (2008)
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)
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)
Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH,
, Molecular Cell, 11/2017, Volume 68, Issue 4, p.797 - 807, (2017)
Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins,
, Structure, Volume 24, p.116 - 126, (2016)
The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA,
, The Journal of Physical Chemistry Letters, 01/01/2017, Volume 8, p.21 - 28, (2017)
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)
SEABED: Small molEcule activity scanner weB servicE baseD.,
, Bioinformatics, 2015 Mar 1, Volume 31, p.773-5, (2015)
Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties,
, Organic Letters, 11/2015, Volume 17, Issue 21, p.5416 - 5419, (2015)
Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor,
, Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields,
, Journal of Chemical Theory and Computation, 2009/09/08, Volume 5, Issue 9, p.2514 - 2530, (2009)
Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA,
, Journal of the American Chemical Society, 12/2016, Volume 138, Issue 50, p.16355 - 16363, (2016)
Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety,
, Nucleic Acids Research, Volume 29, p.2973-2985, (2001)
Solvation enthalpies of neutral solutes in water and octanol,
, Theoretical Chemistry Accounts, 2009/05/01, Volume 123, p.11-20, (2009)
Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures.,
, FEBS J, 2014 Feb, Volume 281, p.1085-99, (2014)
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 basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance,
, Proc. Natl. Acad. Sci, USA, 08/2017, Volume 114, Issue 32, p.E6526 - E6535, (2017)
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.,
, J Mol Biol, 2010 Oct 22, Volume 403, p.217-30, (2010)
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)
The structural impact of DNA mismatches.,
, Nucleic Acids Res, 2015 Apr 30, Volume 43, p.4309-21, (2015)
Structural properties of g,t-parallel duplexes.,
, J Nucleic Acids, 2010, Volume 2010, (2010)
The structure and dynamics of DNA in the gas phase.,
, J Am Chem Soc, 2003 Jul 2, Volume 125, p.8007-14, (2003)
Structure and Dynamics of Oligonucleotides in the Gas Phase,
, Angewandte Chemie International Edition, 01/2015, Volume 54, p.467–471, (2015)
Structure and properties of DNA in apolar solvents,
, J Phys Chem B, 2014 Jul 24, Volume 118, p.8540-8, (2014)