Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions

Strong Reduction of the Chain Rigidity of Hyaluronan by Selective Binding of Ca2+ Ions

(2021) Giulia Giubertoni et al.   MACROMOLECULES

Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data

(2020) Elizabeth K. Whitmore et al.   Biomolecules

Fabrication of chondroitin sulfate calcium complex and its chondrocyte proliferation in vitro

(2020) Qingshan Shen et al.   CARBOHYDRATE POLYMERS

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans

(2020) Serge Pérez et al.   Biomolecules

Promotion effect of immobilized chondroitin sulfate on intrafibrillar mineralization of collagen

(2019) Huihui He et al.   CARBOHYDRATE POLYMERS

Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges

(2018) Andrew Almond   CURRENT OPINION IN STRUCTURAL BIOLOGY

Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization

(2018) Josef Melcr et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions

(2018) Kyungreem Han 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

MatrixDB: integration of new data with a focus on glycosaminoglycan interactions

(2018) Olivier Clerc et al.   NUCLEIC ACIDS RESEARCH

Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation

(2017) Cathy Ng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

(2016) Seonghoon Kim et al.   BIOPHYSICAL JOURNAL

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

(2016) Jejoong Yoo et al.   BIOPOLYMERS

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

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

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger

(2016) Jun Liao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger

(2016) Jun Liao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Proteoglycans and Their Heterogeneous Glycosaminoglycans at the Atomic Scale

(2015) Benedict M. Sattelle et al.   BIOMACROMOLECULES

Molecular interactions between chondroitin–dermatan sulfate and growth factors/receptors/matrix proteins

(2015) Shuji Mizumoto et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides

(2015) Christina E. Faller et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters

(2015) Andrew T. Church et al.   RSC Advances

Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields

(2014) Jens Kahlen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Divalent cation signaling in immune cells

(2014) Benjamin Chaigne-Delalande et al.   TRENDS IN IMMUNOLOGY

POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides

(2013) Søren B. Engelsen et al.   BIOPOLYMERS

Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data

(2013) Richard M. Venable et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The dynamics of the calcium-induced chain-chain association in the polyuronate systems

(2012) Wojciech Plazinski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

(2012) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Chondroitin Sulfate in Solution: Effects of Mono- and Divalent Salts

(2012) Ferenc Horkay et al.   MACROMOLECULES

The influence of extracellular and intracellular calcium on the secretion of renin

(2012) Douglas K. Atchison et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

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

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

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

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

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Additive empirical force field for hexopyranose monosaccharides

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

Parameterization of Ca+2–protein interactions for molecular dynamics simulations

(2007) Elad Project et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY