Revision of the GROMOS 56A6CARBOforce field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations

(2015) Wojciech Plazinski et al.   CARBOHYDRATE RESEARCH

Force fields and scoring functions for carbohydrate simulation

(2015) Xiuming Xiong et al.   CARBOHYDRATE RESEARCH

Kinetic characteristics of conformational changes in the hexopyranose rings

(2015) Wojciech Plazinski et al.   CARBOHYDRATE RESEARCH

Carbohydrate anomalies in the PDB

(2015) Jon Agirre et al.   Nature Chemical Biology

AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems

(2014) Krishna Govender et al.   Journal of Chemical Theory and Computation

Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations

(2014) Krishna K. Govender et al.   Journal of Chemical Theory and Computation

Conformational Diversity of O-Antigen Polysaccharides of the Gram-Negative Bacterium Shigella flexneri Serotype Y

(2014) Yu Kang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational effects due to stereochemistry and C3-substituents in xylopyranoside derivatives as studied by NMR spectroscopy

(2014) Jerk Rönnols et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Microsecond kinetics in model single- and double-stranded amylose polymers

(2014) Benedict M. Sattelle et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Wojciech Plazinski et al.   RSC Advances

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

Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers

(2013) Dongqi Wang et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis

(2013) Heather B. Mayes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exploration of conformational flexibility and hydrogen bonding of xylosides in different solvents, as a model system for enzyme active site interactions

(2013) Jerk Rönnols et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Chair interconversion and reactivity of mannuronic acid esters

(2013) Jerk Rönnols et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Free-energy landscape of protein oligomerization from atomistic simulations

(2013) A. Barducci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates

(2012) Laercio Pol-Fachin et al.   Journal of Chemical Theory and Computation

Dependence of Pyranose Ring Puckering on Anomeric Configuration: Methyl Idopyranosides

(2012) Benedict M. Sattelle et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Synthesis, conformation and biology of naphthoxylosides

(2011) Anna Siegbahn et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

(2011) Nathan Schmid et al.   COMPUTER PHYSICS COMMUNICATIONS

pKa-Determination and Conformational Studies by NMR Spectroscopy of D-Altrose-Containing and other Pseudodisaccharides as Glycosidase Inhibitor Candidates

(2011) Jerk Rönnols et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

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

(2011) Benedict M Sattelle et al.   GLYCOBIOLOGY

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

(2011) Bruno A. C. Horta et al.   Journal of Chemical Theory and Computation

New functionalities in the GROMOS biomolecular simulation software

(2011) Anna-Pitschna E. Kunz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hyperconjugation

(2011) Igor V. Alabugin et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Carbohydrate force fields

(2011) B. Lachele Foley et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Linking Well-Tempered Metadynamics Simulations with Experiments

(2010) Alessandro Barducci et al.   BIOPHYSICAL JOURNAL

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

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

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

Conformational pathways of simple six-membered rings

(2010) Carlos A. Stortz   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

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

DFTMD studies of glucose and epimers: anomeric ratios, rotamer populations, and hydration energies

(2009) U. Schnupf 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

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

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

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

Mechanistic insights into glycosidase chemistry

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

Disaccharide conformational maps: adiabaticity in analogues with variable ring shapes

(2008) Carlos A. Stortz 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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Structure and dynamics of maltooligomer–water solutions and glasses

(2008) Hans Jörg Limbach et al.   Soft Matter

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