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

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling

(2010) Lovorka Perić-Hassler et al.   CARBOHYDRATE RESEARCH

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

(2010) E. Autieri 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

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

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

Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex

(2010) Hiroko Satoh et al.   Journal of Chemical Theory and Computation

Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection

(2010) Daan P. Geerke et al.   MOLECULAR SIMULATION

GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations

(2009) Laercio Pol-Fachin et al.   CARBOHYDRATE RESEARCH

Comparison of different force fields for the study of disaccharides

(2009) Carlos A. Stortz et al.   CARBOHYDRATE RESEARCH

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

(2009) Vojtěch Spiwok et al.   CARBOHYDRATE RESEARCH

On the calculation of puckering free energy surfaces

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

Martini Coarse-Grained Force Field: Extension to Carbohydrates

(2009) Cesar A. López et al.   Journal of Chemical Theory and Computation

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

(2009) Olgun Guvench et al.   Journal of Chemical Theory and Computation

Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials

(2009) Jason B. Brokaw et al.   Journal of Chemical Theory and Computation

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol

(2009) Elizabeth R. Hatcher et al.   Journal of Chemical Theory and Computation

Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS)

(2009) Clara D. Christ et al.   Journal of Chemical Theory and Computation

Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation

(2009) Clara D. Christ et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose

(2009) Elizabeth Hatcher et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Gel-Like Structure of a Hexadecyl Derivative of Hyaluronic Acid for the Treatment of Osteoarthritis

(2009) Ivana Finelli et al.   MACROMOLECULAR BIOSCIENCE

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

Mechanical Properties of C-5 Epimerized Alginates

(2008) Ý. A. Mørch et al.   BIOMACROMOLECULES

Effect of Trehalose on a Phospholipid Membrane under Mechanical Stress

(2008) Cristina S. Pereira et al.   BIOPHYSICAL JOURNAL

Kinetics of conformer formation of glucose and maltose in aqueous solutions

(2008) Julian Haller et al.   CHEMICAL PHYSICS LETTERS

Carbohydrate Polymers at the Center of Life’s Origins: The Importance of Molecular Processivity

(2008) Robert Stern et al.   CHEMICAL REVIEWS

Mechanistic insights into glycosidase chemistry

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

Molecular modeling of interfaces between cellulose crystals and surrounding molecules: Effects of caprolactone surface grafting

(2008) Malin Bergenstråhle et al.   EUROPEAN POLYMER JOURNAL

Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions

(2008) Clara D. Christ et al.   JOURNAL OF CHEMICAL PHYSICS

Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

(2008) Eduardo F. Franca et al.   Journal of Chemical Theory and Computation

Additive empirical force field for hexopyranose monosaccharides

(2008) Olgun Guvench et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Interaction between the CBM of Cel9A fromThermobifida fuscaand cellulose fibers

(2008) Osmair V. Oliveira et al.   JOURNAL OF MOLECULAR RECOGNITION

Identification of the Molecular Motions Responsible for the Slower Secondary (β) Relaxation in Sucrose

(2008) K. Kaminski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sampling of Rare Events Using Hidden Restraints

(2008) Markus Christen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics of Cellulose−Water Interfaces:  NMR Spin−Lattice Relaxation Times Calculated from Atomistic Computer Simulations

(2008) Malin Bergenstråhle et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dielectric Studies on Mobility of the Glycosidic Linkage in Seven Disaccharides

(2008) K. Kaminski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The influence of polyhydroxylated compounds on a hydrated phospholipid bilayer: a molecular dynamics study

(2008) Cristina S. Pereira et al.   MOLECULAR SIMULATION

Conformation, dynamics and ion-binding properties of single-chain polyuronates: a molecular dynamics study

(2008) Lovorka Perić et al.   MOLECULAR SIMULATION

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

Complete assignments of the 1H and 13C chemical shifts and JH,H coupling constants in NMR spectra of d-glucopyranose and all d-glucopyranosyl-d-glucopyranosides

(2007) Mattias U. Roslund et al.   CARBOHYDRATE RESEARCH

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