Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations

(2021) Gábor Balogh et al.   Journal of Chemical Information and Modeling

Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides

(2019) Gábor Balogh et al.   Journal of Chemical Information and Modeling

Extension of the GROMOS 56a6CARBO/CARBO_R Force Field for Charged, Protonated, and Esterified Uronates

(2018) Karina Panczyk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans

(2016) Arunima Singh et al.   CANADIAN JOURNAL OF CHEMISTRY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Solution Structure of Heparin Pentasaccharide: NMR and DFT Analysis

(2015) Miloš Hricovíni   JOURNAL OF PHYSICAL CHEMISTRY B

NMR Chemical Shifts in Structural Biology of Glycosaminoglycans

(2013) Vitor H. Pomin   ANALYTICAL CHEMISTRY

Glycosaminoglycans in infectious disease

(2013) Eyal Kamhi et al.   BIOLOGICAL REVIEWS

Mapping of heparin/heparan sulfate binding sites on αvβ3 integrin by molecular docking

(2013) Lionel Ballut et al.   JOURNAL OF MOLECULAR RECOGNITION

Toward an Accurate Conformational Modeling of Iduronic Acid

(2013) Pavel Oborský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sulfamate proton solvent exchange in heparin oligosaccharides: Evidence for a persistent hydrogen bond in the antithrombin-binding pentasaccharide Arixtra

(2012) Derek J Langeslay et al.   GLYCOBIOLOGY

Dependence of Pyranose Ring Puckering on Anomeric Configuration: Methyl Idopyranosides

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

How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics

(2011) Mauricio GS Costa et al.   BMC GENOMICS

Conformational Selection of the AGA*IAM Heparin Pentasaccharide when Bound to the Fibroblast Growth Factor Receptor

(2011) Lidia Nieto et al.   CHEMISTRY-A EUROPEAN JOURNAL

CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

(2011) Olgun Guvench et al.   Journal of Chemical Theory and Computation

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

Free energy calculations of glycosaminoglycan–protein interactions

(2009) Neha S Gandhi et al.   GLYCOBIOLOGY

Residual dipolar coupling investigation of a heparin tetrasaccharide confirms the limited effect of flexibility of the iduronic acid on the molecular shape of heparin

(2009) L. Jin et al.   GLYCOBIOLOGY

Langevin thermostat for rigid body dynamics

(2009) Ruslan L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM: The biomolecular simulation program

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

Depiction of the forces participating in the 2-O-sulfo-α-l-iduronic acid conformational preference in heparin sequences in aqueous solutions

(2008) Laercio Pol-Fachin et al.   CARBOHYDRATE RESEARCH