Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations

The effect of interleukin-8 truncations on its interactions with glycosaminoglycans

(2018) Karoline Nordsieck et al.   BIOPOLYMERS

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

(2018) Andrew Almond   CURRENT OPINION IN STRUCTURAL BIOLOGY

So you think computational approaches to understanding glycosaminoglycan–protein interactions are too dry and too rigid? Think again!

(2018) Nehru Viji Sankaranarayanan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Reparameterization of Solute—Solute Interactions for Amino Acid–Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

(2017) Wesley K. Lay et al.   Journal of Chemical Theory and Computation

Atomistic fingerprint of hyaluronan–CD44 binding

(2017) Joni Vuorio et al.   PLoS Computational Biology

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

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

Computational analysis of interactions in structurally available protein–glycosaminoglycan complexes

(2016) Sergey A Samsonov et al.   GLYCOBIOLOGY

Computational drill down on FGF1-heparin interactions through methodological evaluation

(2016) Sándor Babik et al.   GLYCOCONJUGATE JOURNAL

Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions

(2015) P. R. B. Joseph et al.   BIOCHEMICAL JOURNAL

Proteoglycans and Their Heterogeneous Glycosaminoglycans at the Atomic Scale

(2015) Benedict M. Sattelle et al.   BIOMACROMOLECULES

The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 Is Modulated by Sulfation Pattern and pH

(2015) Arunima Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Glycosaminoglycan derivatives: promising candidates for the design of functional biomaterials

(2015) Dieter Scharnweber et al.   JOURNAL OF MATERIALS SCIENCE-MATERIALS IN MEDICINE

Chemokines and Glycosaminoglycans

(2015) Amanda E. I. Proudfoot   Frontiers in Immunology

Sulfated Glycosaminoglycans Exploit the Conformational Plasticity of Bone Morphogenetic Protein-2 (BMP-2) and Alter the Interaction Profile with Its Receptor

(2014) Vera Hintze et al.   BIOMACROMOLECULES

Importance of the polarity of the glycosaminoglycan chain on the interaction with FGF-1

(2014) Juan C Muñoz-García et al.   GLYCOBIOLOGY

Multipose Binding in Molecular Docking

(2014) Kalina Atkovska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5

(2014) Jagdish Suresh Patel et al.   Journal of Chemical Information and Modeling

Coarse-Grained Model of Glycosaminoglycans

(2014) Sergey A. Samsonov et al.   Journal of Chemical Information and Modeling

Does Microsecond Sugar Ring Flexing Encode 3D-Shape and Bioactivity in the Heparanome?

(2013) Benedict M. Sattelle et al.   BIOMACROMOLECULES

Importance of IdoA and IdoA(2S) ring conformations in computational studies of glycosaminoglycan–protein interactions

(2013) Sergey A. Samsonov et al.   CARBOHYDRATE RESEARCH

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

(2013) M. Gur et al.   JOURNAL OF CHEMICAL PHYSICS

Computational Design of New Peptide Inhibitors for Amyloid Beta (Aβ) Aggregation in Alzheimer's Disease: Application of a Novel Methodology

(2013) Gözde Eskici et al.   PLoS One

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling

(2011) Annelie Pichert et al.   GLYCOBIOLOGY

Molecular Dynamics Simulations of CXCL-8 and Its Interactions with a Receptor Peptide, Heparin Fragments, and Sulfated Linked Cyclitols

(2011) Neha S. Gandhi et al.   Journal of Chemical Information and Modeling

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

(2011) Sergey A. Samsonov et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Free energy calculations of glycosaminoglycan–protein interactions

(2009) Neha S Gandhi et al.   GLYCOBIOLOGY

Semi-Rigid Solution Structures of Heparin by Constrained X-ray Scattering Modelling: New Insight into Heparin–Protein Complexes

(2009) Sanaullah Khan et al.   JOURNAL OF MOLECULAR BIOLOGY

The FGF family: biology, pathophysiology and therapy

(2009) Andrew Beenken et al.   NATURE REVIEWS DRUG DISCOVERY

Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex

(2008) Harish Vashisth et al.   BIOPHYSICAL JOURNAL

Endocrine FGFs and Klothos: emerging concepts

(2008) Makoto Kuro-o   TRENDS IN ENDOCRINOLOGY AND METABOLISM