Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans

Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study

(2020) Krzysztof K. Bojarski et al.   Journal of Chemical Information and Modeling

Prediction of protein–protein complexes using replica exchange with repulsive scaling

(2020) Till Siebenmorgen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Glycosaminoglycan–Protein Interactions: The First Draft of the Glycosaminoglycan Interactome

(2020) Sylvain D. Vallet et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Characterization of heparin and severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) spike glycoprotein binding interactions

(2020) So Young Kim et al.   ANTIVIRAL RESEARCH

Efficient Refinement and Free Energy Scoring of Predicted Protein–Protein Complexes Using Replica Exchange with Repulsive Scaling

(2020) Till Siebenmorgen et al.   Journal of Chemical Information and Modeling

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

Glycosaminoglycans and Glycosaminoglycan Mimetics in Cancer and Inflammation

(2019) Shravan Morla   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Glycosaminoglycans: a link between development and regeneration in the lung

(2019) Jenny Cecilia Wigén et al.   STEM CELLS AND DEVELOPMENT

Docking software performance in protein-glycosaminoglycan systems

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

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

(2019) Potthoff et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Rat cathepsin K: Enzymatic specificity and regulation of its collagenolytic activity

(2019) Fabien Lecaille et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Glycobiology of syndecan-1 in bacterial infections

(2018) Rafael S. Aquino et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2018) Andrew Almond   CURRENT OPINION IN STRUCTURAL BIOLOGY

Specificity of glycosaminoglycan–protein interactions

(2018) Lena Kjellén et al.   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

Glycosaminoglycans have variable effects on α-synuclein aggregation and differentially affect the activities of the resulting amyloid fibrils

(2018) Surabhi Mehra et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The sulfation code for propagation of neurodegeneration

(2018) Masahito Yamada et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteoglycan Chemical Diversity Drives Multifunctional Cell Regulation and Therapeutics

(2018) Nikos K. Karamanos et al.   CHEMICAL REVIEWS

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

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

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans

(2017) Alan Cartmell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomistic fingerprint of hyaluronan–CD44 binding

(2017) Joni Vuorio et al.   PLoS Computational Biology

Regioselective sulfation of Artemisia sphaerocephala polysaccharide: Solution conformation and antioxidant activities in vitro

(2016) Junlong Wang et al.   CARBOHYDRATE POLYMERS

Epidermal growth factor loaded heparin-based hydrogel sheet for skin wound healing

(2016) MeeiChyn Goh et al.   CARBOHYDRATE POLYMERS

Chemoenzymatic Synthesis of Nonasulfated Tetrahyaluronan with a Paramagnetic Tag for Studying Its Complex with Interleukin-10

(2016) Sebastian Köhling et al.   CHEMISTRY-A EUROPEAN JOURNAL

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

Fell-Muir Lecture: Heparan sulphate and the art of cell regulation: a polymer chain conducts the protein orchestra

(2015) John Gallagher   INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY

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

Heparin/Heparan Sulfate Proteoglycans Glycomic Interactome in Angiogenesis: Biological Implications and Therapeutical Use

(2015) Paola Chiodelli et al.   MOLECULES

Chemokines and Glycosaminoglycans

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

Demystifying Heparan Sulfate–Protein Interactions

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

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

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

Coarse-Grained Model of Glycosaminoglycans

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

Structural basis of collagen fiber degradation by cathepsin K

(2014) Adeleke H. Aguda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Improved Generalized Born Solvent Model Parameters for Protein Simulations

(2013) Hai Nguyen et al.   Journal of Chemical Theory and Computation

Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles

(2013) Katja Ostermeir et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural insights into proteoglycan-shaped Hedgehog signaling

(2013) D. M. Whalen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Residue 75 of Interleukin-8 is Crucial for its Interactions with Glycosaminoglycans

(2012) Karoline Nordsieck et al.   CHEMBIOCHEM

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

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

Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism

(2010) J. Herrou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Snapshots of Heparin Depolymerization by Heparin Lyase I

(2009) Young-Hyun Han et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Interplay between Endostatin, Integrins, and Heparan Sulfate

(2009) Clément Faye et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 fromAzotobacter vinelandii

(2008) Henriëtte J. Rozeboom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

The Crystal and Molecular Structures of a Cathepsin K:Chondroitin Sulfate Complex

(2008) Zhenqiang Li et al.   JOURNAL OF MOLECULAR BIOLOGY