Estimating glycosaminoglycan–protein interaction affinity: water dominates the specific antithrombin–heparin interaction

Chemoenzymatically Prepared Heparan Sulfate Containing Rare 2-O-Sulfonated Glucuronic Acid Residues

(2015) Rio S. Boothello et al.   ACS Chemical Biology

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

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Simple Method for Discovering Druggable, Specific Glycosaminoglycan-Protein Systems. Elucidation of Key Principles from Heparin/Heparan Sulfate-Binding Proteins

(2015) Aurijit Sarkar et al.   PLoS One

Demystifying Heparan Sulfate–Protein Interactions

(2014) Ding Xu et al.   Annual Review of Biochemistry

Toward a robust computational screening strategy for identifying glycosaminoglycan sequences that display high specificity for target proteins

(2014) Nehru Viji Sankaranarayanan et al.   GLYCOBIOLOGY

Docking Server for the Identification of Heparin Binding Sites on Proteins

(2014) Scott E. Mottarella et al.   Journal of Chemical Information and Modeling

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

On the Specificity of Heparin/Heparan Sulfate Binding to Proteins. Anion-Binding Sites on Antithrombin and Thrombin Are Fundamentally Different

(2012) Philip D. Mosier et al.   PLoS One

Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-β-d-glucuronidase (heparanase)

(2011) Neha S Gandhi et al.   GLYCOBIOLOGY

Molecular modeling of the interaction between heparan sulfate and cellular growth factors: Bringing pieces together

(2011) Nicolas Sapay et al.   GLYCOBIOLOGY

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

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

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

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

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

Understanding Dermatan Sulfate−Heparin Cofactor II Interaction through Virtual Library Screening

(2010) Arjun Raghuraman et al.   ACS Medicinal Chemistry Letters

Free energy calculations of glycosaminoglycan–protein interactions

(2009) Neha S Gandhi et al.   GLYCOBIOLOGY

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

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

Application of drug discovery software to the identification of heparin-binding sites on protein surfaces: a computational survey of the 4-helix cytokines

(2008) Barbara Mulloy et al.   MOLECULAR SIMULATION