Biblio
pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs,
, Journal of the American Chemical Society, 02/2023, Volume 145, Issue 6, p.3696 - 3705, (2023)
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case,
, WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)
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)
Probing allosteric regulations with coevolution-driven molecular simulations,
, Science advances, 10/2021, Volume 7, Issue 37, p.eabj0786 - eabj0786, (2021)
Predicting the limit of intramolecular H-Bonding with classical molecular dynamics,
, Angewandte Chemie International Edition, 01/2019, (2019)
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)
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)
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)
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)
Principles for designing proteins with cavities formed by curved β sheets,
, Science (New York, N.Y.), 01/2017, Volume 355, Issue 6321, p.201 - 206, (2017)
Proton Dynamics in Protein Mass Spectrometry,
, The Journal of Physical Chemistry Letters, 03/2017, Volume 8, Issue 6, p.1105 - 1112, (2017)
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations,
, Nat Commun, 2016/08/31, Volume 7, (2016)
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data,
, SoftwareX, 12/2016, Volume 5, p.44 - 50, (2016)
PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.,
, J Chem Theory Comput, 2015 Dec 8, Volume 11, p.5929-38, (2015)
Proteins in the gas phase,
, WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)
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)
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)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.,
, Proteins, 2010 Jan, Volume 78, p.83-94, (2010)
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)
A procedure for identifying homologous alternative splicing events.,
, BMC Bioinformatics, 2007, Volume 8, p.260, (2007)
Partition of protein solvation into group contributions from molecular dynamics simulations.,
, Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)
PMUT: a web-based tool for the annotation of pathological mutations on proteins.,
, Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)
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)
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines.,
, Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)