Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

(2012) Mahmoud Moradi et al.   PLoS Computational Biology

A Statistical Analysis of the PPII Propensity of Amino Acid Guests in Proline-Rich Peptides

(2011) Mahmoud Moradi et al.   BIOPHYSICAL JOURNAL

Calculating relative transition rates with driven nonequilibrium simulations

(2011) Mahmoud Moradi et al.   CHEMICAL PHYSICS LETTERS

Dynamic phase transition in the conversion of B-DNA to Z-DNA

(2011) Jaya Maji et al.   EPL

PPII Propensity of Multiple-Guest Amino Acids in a Proline-Rich Environment

(2011) Mahmoud Moradi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

(2010) Mahmoud Moradi et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

(2010) Mahmoud Moradi et al.   JOURNAL OF CHEMICAL PHYSICS

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

(2010) Volodymyr Babin et al.   JOURNAL OF CHEMICAL PHYSICS

Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation

(2010) Juyong Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Two distinct overstretched DNA states

(2010) Hongxia Fu et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of a junction between two Z-DNA helices

(2010) M. de Rosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

(2009) Volodymyr Babin et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Conformations and free energy landscapes of polyproline peptides

(2009) M. Moradi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptively biased molecular dynamics for free energy calculations

(2008) Volodymyr Babin et al.   JOURNAL OF CHEMICAL PHYSICS

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols