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
Published 2010 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
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
Authors
Keywords
-
Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 32, Issue 6, Pages 998-1032
Publisher
Wiley
Online
2010-11-10
DOI
10.1002/jcc.21675
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now