Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse

Comparison of Carbohydrate Force Fields in Molecular Dynamics Simulations of Protein–Carbohydrate Complexes

(2021) Anita Plazinska et al.   Journal of Chemical Theory and Computation

Glycosidic linkage flexibility: The ψ torsion angle has a bimodal distribution in α-L-Rhap-(1→2)-α-L-Rhap-OMe as deduced from 13C NMR spin relaxation

(2020) Mirco Zerbetto et al.   JOURNAL OF CHEMICAL PHYSICS

Use of Circular Statistics To Model αMan-(1→2)-αMan and αMan-(1→3)-α/βMan O-Glycosidic Linkage Conformation in 13C-Labeled Disaccharides and High-Mannose Oligosaccharides

(2019) Wenhui Zhang et al.   BIOCHEMISTRY

A GROMOS Force Field for Furanose-Based Carbohydrates

(2019) Karina Nester et al.   Journal of Chemical Theory and Computation

Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives

(2019) Poonam Pandey et al.   Journal of Chemical Theory and Computation

A Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields

(2019) Jaya Krishna Koneru et al.   Journal of Chemical Theory and Computation

Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

(2019) Michael C. Owen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses

(2018) Asaminew H. Aytenfisu et al.   Journal of Chemical Theory and Computation

Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution

(2018) Julia Gebhardt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

(2018) Jejoong Yoo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Comparison of the simulations of cellulosic crystals with three carbohydrate force fields

(2016) Hitomi Miyamoto et al.   CARBOHYDRATE RESEARCH

Conformational Dynamics of the Single Lipopolysaccharide O-Antigen in Solution

(2016) Tatiana Galochkina et al.   CHEMPHYSCHEM

Optimizing Solute–Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements

(2016) Wesley K. Lay et al.   Journal of Chemical Theory and Computation

Predicting the Chemical Potential and Osmotic Pressure of Polysaccharide Solutions by Molecular Simulations

(2016) Jörg Sauter et al.   Journal of Chemical Theory and Computation

CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures

(2016) Michelle M. Kuttel et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Solution conformation and flexibility of capsular polysaccharides from Neisseria meningitidis and glycoconjugates with the tetanus toxoid protein

(2016) Ali Saber Abdelhameed et al.   Scientific Reports

Solution Properties of Hemicellulose Polysaccharides with Four Common Carbohydrate Force Fields

(2015) Jörg Sauter et al.   Journal of Chemical Theory and Computation

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

(2015) Wojciech Plazinski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

(2015) Madhurima Jana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields

(2014) Michelle Kuttel et al.   CARBOHYDRATE RESEARCH

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

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator

(2014) Dhilon S. Patel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations

(2012) Mona Zaccheus et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields

(2012) James F. Matthews et al.   Journal of Chemical Theory and Computation

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

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

Studies on the conformational flexibility of α-l-rhamnose-containing oligosaccharides using 13C-site-specific labeling, NMR spectroscopy and molecular simulations: implications for the three-dimensional structure of bacterial rhamnan polysaccharides

(2012) K. Hanna M. Jonsson et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

(2011) Sairam S. Mallajosyula et al.   Journal of Chemical Theory and Computation

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects

(2010) Elisa Fadda et al.   DRUG DISCOVERY TODAY

CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses

(2010) E. Prabhu Raman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2009) Vojtěch Spiwok et al.   CARBOHYDRATE RESEARCH

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

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

Visualisation of cyclic and multi-branched molecules with VMD

(2009) Simon Cross et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Additive empirical force field for hexopyranose monosaccharides

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