Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction

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

(2019) Sergey A. Samsonov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2019) Krzysztof K. Bojarski et al.   BIOPOLYMERS

Docking software performance in protein-glycosaminoglycan systems

(2019) Urszula Uciechowska-Kaczmarzyk et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

Structural Basis for the Acceleration of Procollagen Processing by Procollagen C-Proteinase Enhancer-1

(2018) David Pulido et al.   STRUCTURE

Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners

(2018) Sylvain D. Vallet et al.   Scientific Reports

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information

(2017) Agnieszka S. Karczyńska et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural and functional insights into the interaction of sulfated glycosaminoglycans with tissue inhibitor of metalloproteinase-3 – A possible regulatory role on extracellular matrix homeostasis

(2016) Sandra Rother et al.   Acta Biomaterialia

Recognizing metal and acid radical ion-binding sites by integratingab initiomodeling with template-based transferals

(2016) Xiuzhen Hu et al.   BIOINFORMATICS

Computational analysis of interactions in structurally available protein–glycosaminoglycan complexes

(2016) Sergey A Samsonov et al.   GLYCOBIOLOGY

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

BMP-1/tolloid-like proteinases synchronize matrix assembly with growth factor activation to promote morphogenesis and tissue remodeling

(2015) Sandrine Vadon-Le Goff et al.   MATRIX BIOLOGY

Chemokines and Glycosaminoglycans

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

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

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

(2014) Adam Liwo et al.   JOURNAL OF MOLECULAR MODELING

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

(2013) Benedict M. Sattelle et al.   BIOMACROMOLECULES

Investigation of lysine side chain interactions of interleukin-8 with heparin and other glycosaminoglycans studied by a methylation-NMR approach

(2013) K. Mobius et al.   GLYCOBIOLOGY

Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff

(2013) Anita K. Nivedha et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2012) Nadine Homeyer et al.   Molecular Informatics

Structure and properties of the Ca2+-binding CUB domain, a widespread ligand-recognition unit involved in major biological functions

(2011) Christine Gaboriaud et al.   BIOCHEMICAL JOURNAL

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

Biologically relevant metal-cation binding induces conformational changes in heparin oligosaccharides as measured by ion mobility mass spectrometry

(2011) Youjin Seo et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Binding of Heparin to Metals

(2010) Ivan Stevic et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Role of the Netrin-like Domain of Procollagen C-Proteinase Enhancer-1 in the Control of Metalloproteinase Activity

(2010) Mourad Bekhouche et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Binding of Procollagen C-Proteinase Enhancer-1 (PCPE-1) to Heparin/Heparan Sulfate

(2010) Tali Weiss et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Free energy calculations of glycosaminoglycan–protein interactions

(2009) Neha S Gandhi et al.   GLYCOBIOLOGY

Basement membrane proteoglycans: Modulators Par Excellence of cancer growth and angiogenesis

(2009) Renato V. Iozzo et al.   MOLECULES AND CELLS

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY