June 26, 2012

Publications

Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes.
BBRC, 2017. Link to Article

MD Simulations of Virus-Like Particles with Supra CG solvation affordable to desktop computers.
JCTC, 2017. Link to Article

Modeling DMPC lipid membranes with SIRAH force-field.
J. Mol. Model., 2017. Link to Article

The ataxia related G1107D mutation of the plasma membrane Ca2 + ATPase isoform 3 affects its interplay with calmodulin and the autoinhibition process.
BBA-Mol. Basis Dis., 2016. Link to Article

SIRAH Tools: mapping, backmapping and visualization of coarse-grained models.
Bioinformatics, 2016. Link to Article

Exploring LacI-DNA Dynamics by Multiscale Simulations Using the SIRAH Force Field.
JCTC, 2015. Link to Article

SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. 
JCTC, 2015. Link to Article

Transferable Mixing of Atomistic and Coarse-Grained Water Models.

J. Phys. Chem. 2013. Link to Article

Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level.
Lect. Notes in Comp. Science, 2013. Link to Article

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations.
Phys. Rev. Lett. 2012. Link to Article

Coarse-grained models of water.

WIREs Comput Mol Sci, 2012. Link to Article

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations:
Let WT4 Handle the Bulk.

JCTC, 2012. Link to Article

A hybrid all-atom/coarse grain model for multiscale simulations of DNA.

PCCP, 2011. Link to Article

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics.

JCTC, 2010. Link to Article

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

JCTC, 2010. Link to Article