Modeling large protein-glycosaminoglycan complexes using a fragment-based approach

Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth

(2017) Adam R. Griffith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Glycosaminoglycan derivatives: promising candidates for the design of functional biomaterials

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

Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry

(2015) Tommy Hofmann et al.   METHODS

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

Development and application of site mapping methods for the design of glycosaminoglycans

(2014) Mark Agostino et al.   GLYCOBIOLOGY

Flexibility and Explicit Solvent in Molecular-Dynamics-Based Docking of Protein–Glycosaminoglycan Systems

(2014) Sergey A. Samsonov 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

AutoMap: A tool for analyzing protein–ligand recognition using multiple ligand binding modes

(2013) Mark Agostino et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Sampling and scoring: A marriage made in heaven

(2013) Sandor Vajda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Undersulfation of Heparan Sulfate Restricts Differentiation Potential of Mouse Embryonic Stem Cells

(2012) Maud Forsberg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Heparan Sulfate Facilitates FGF and BMP Signaling to Drive Mesoderm Differentiation of Mouse Embryonic Stem Cells

(2012) Daniel C. Kraushaar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches

(2011) C. J. Rogers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward a Robust Search Method for the Protein-Drug Docking Problem

(2010) B S Sadjad et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design

(2009) Takashi Imai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In silico analysis of antibody–carbohydrate interactions and its application to xenoreactive antibodies

(2009) Mark Agostino et al.   MOLECULAR IMMUNOLOGY