Publications
] .
2020. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.. J Chem Phys. 153(5):050901.
.
1985. On the possible mechanism of multiple enzyme attack in polysaccharide degradation. Mol. Biol.. 19:1400–1408.
.
2019. The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements. Nucleic Acids Res. 47:1836-1846.
.
2003. The position of Q B in the photosynthetic reaction center depends on pH: A theoretical analysis of the proton uptake upon Q B reduction. Biophys. J.. 84:2090–2098.
.
1990. Pore formation kinetics in membranes, determined from the release of marker molecules out of liposomes or cells. Biophys. J.. 58:577–583.
.
2015. The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo. Nucleic Acids Res.. 43:6473–85.
.
2015. Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study. Phys. Chem. Chem. Phys.. 17:27275–27280.
.
2016. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses. Phys. Chem. Chem. Phys.. 18:11951–11958.
.
2015. Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. J. Chem. Phys.. 143:155101.
.
2019. Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion. 49:234–244.
.
2006. Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study. Biophys. J.. 91:1224–1234.
.
2024. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model. 64:26–41.
.
1993. Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers. 33:335–50.
.
2016. PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res.. 44:W449-W454.
.
2012. PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res.. 40:W288-W293.
.
2009. PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res.. 37:W498-W503.
.
2009. PEP-FOLD: an online resource for de novo peptide structure prediction.. Nucleic Acids Res.. 37:W498–W503.
.
2004. Pathway complexity of Alzheimer's beta-amyloid A beta(16-22) peptide assembly. Structure. 12:1245–1255.
.
2007. Probing amyloid fibril formation of the NFGAIL peptide by computer simulations. J. Chem. Phys.. 126:065101.
.
2015. Predicting and exploring complex nucleic acids architectures through a coarse-grained model. J. Biomol. Struct. Dyn.. 33 Suppl 1:30–31.
.
2010. Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
.
1987. Oxygen binding constants for human hemoglobin tetramers. Biochemistry. 26:3995–4002.
.
2004. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J. Chem. Phys.. 121:2904–2914.
.
2008. Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. European Biophysics Journal with Biophysics Letters. 37:131–141.
.
2013. On the origin of thermal untwisting of DNA. J. Phys. Chem. B. 117:1857–1861.