The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Does Microsecond Sugar Ring Flexing Encode 3D-Shape and Bioactivity in the Heparanome?

(2013) Benedict M. Sattelle et al.   BIOMACROMOLECULES

The dynamics of the calcium-induced chain-chain association in the polyuronate systems

(2012) Wojciech Plazinski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Is N-acetyl-d-glucosamine a rigid 4C1 chair?

(2011) Benedict M Sattelle et al.   GLYCOBIOLOGY

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

(2010) E. Autieri et al.   JOURNAL OF CHEMICAL PHYSICS

Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries

(2010) Halvor S. Hansen et al.   Journal of Chemical Theory and Computation

A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers

(2010) Halvor S. Hansen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations

(2010) Christopher B. Barnett et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy Landscapes of Iduronic Acid and Related Monosaccharides

(2010) Benedict M. Sattelle et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pickett angles and Cremer–Pople coordinates as collective variables for the enhanced sampling of six-membered ring conformations

(2010) M. Sega et al.   MOLECULAR PHYSICS

Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein

(2010) J. Vreede et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modelling of β-d-glucopyranose ring distortion in different force fields: a metadynamics study

(2009) Vojtěch Spiwok et al.   CARBOHYDRATE RESEARCH

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

On the calculation of puckering free energy surfaces

(2009) M. Sega et al.   JOURNAL OF CHEMICAL PHYSICS

Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water

(2009) Halvor S. Hansen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational Free Energy Surface of α-N-Acetylneuraminic Acid: An Interplay Between Hydrogen Bonding and Solvation

(2009) Vojtěch Spiwok et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

(2009) Luis Petersen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Force Pulling of Single Cellulose Chains at the Crystalline Cellulose−Liquid Interface: A Molecular Dynamics Study

(2009) Malin Bergenstråhle et al.   LANGMUIR

Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): an application to ring puckering

(2009) Christopher B. Barnett et al.   MOLECULAR PHYSICS

Mechanism of glycoside hydrolysis: A comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases

(2009) Mahmoud E. S. Soliman et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

(2008) Jarek Juraszek et al.   BIOPHYSICAL JOURNAL

Mechanistic insights into glycosidase chemistry

(2008) David J Vocadlo et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases

(2008) Mahmoud E. S. Soliman et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Stretching single polysaccharide molecules using AFM: A potential method for the investigation of the intermolecular uronate distribution of alginate?

(2007) Martin A.K. Williams et al.   FOOD HYDROCOLLOIDS

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation