A Bittersweet Computational Journey among Glycosaminoglycans

A Systems View of the Heparan Sulfate Interactome

(2021) Alejandro Gómez Toledo et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Heparan Sulfate Glycosaminoglycans: (Un)Expected Allies in Cancer Clinical Management

(2021) Isabel Faria-Ramos et al.   Biomolecules

HS and Inflammation: A Potential Playground for the Sulfs?

(2020) Rana El Masri et al.   Frontiers in Immunology

Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data

(2020) Elizabeth K. Whitmore et al.   Biomolecules

Molecular Interactions Stabilizing the Promatrix Metalloprotease-9·Serglycin Heteromer

(2020) Rangita Dawadi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Analysis of the Glycosaminoglycan Chains of Proteoglycans

(2020) Yuefan Song et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

The Role of Glypicans in Cancer Progression and Therapy

(2020) Nan Li et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

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

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

Tools for generating and analyzing glycan microarray data

(2020) Akul Y Mehta et al.   Beilstein Journal of Organic Chemistry

Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics

(2020) Elizabeth K. Whitmore et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Heparan Sulfate Proteoglycans Biosynthesis and Post Synthesis Mechanisms Combine Few Enzymes and Few Core Proteins to Generate Extensive Structural and Functional Diversity

(2020) Thibault Annaval et al.   MOLECULES

Cell-surface heparan sulfate proteoglycans as multifunctional integrators of signaling in cancer

(2020) Nourhan Hassan et al.   CELLULAR SIGNALLING

Heparanase and the hallmarks of cancer

(2020) Krishnath M. Jayatilleke et al.   Journal of Translational Medicine

Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication

(2020) Benjamin P. Kellman et al.   TRENDS IN BIOCHEMICAL SCIENCES

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans

(2020) Serge Pérez et al.   Biomolecules

Glycosaminoglycans in Tissue Engineering: A Review

(2020) Harkanwalpreet Sodhi et al.   Biomolecules

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

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

Structures and interactions of syndecans

(2019) Frank Gondelaud et al.   FEBS Journal

Docking software performance in protein-glycosaminoglycan systems

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

Heparan Sulfate Proteoglycans and Viral Attachment: True Receptors or Adaptation Bias?

(2019) Cagno et al.   Viruses-Basel

Molecular Docking: Shifting Paradigms in Drug Discovery

(2019) Luca Pinzi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Hyaluronic acid: A review on its biology, aspects of drug delivery, route of administrations and a special emphasis on its approved marketed products and recent clinical studies

(2019) Shyam Vasvani et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Heparin and heparan sulfate proteoglycans promote HIV-1 p17 matrix protein oligomerization: computational, biochemical and biological implications

(2019) Antonella Bugatti et al.   Scientific Reports

Biolubrication synergy: Hyaluronan – Phospholipid interactions at interfaces

(2019) Andra Dėdinaitė et al.   ADVANCES IN COLLOID AND INTERFACE SCIENCE

Interactions of a short hyaluronan chain with a phospholipid membrane

(2019) Piotr Bełdowski et al.   COLLOIDS AND SURFACES B-BIOINTERFACES

Recent advances in glycoinformatic platforms for glycomics and glycoproteomics

(2019) Jodie L Abrahams et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Hyaluronan-Chondroitin Sulfate Anomalous Crosslinking Due to Temperature Changes

(2018) Tomasz Andrysiak et al.   Polymers

The Anomalies of Hyaluronan Structures in Presence of Surface Active Phospholipids—Molecular Mass Dependence

(2018) Piotr Bełdowski et al.   Polymers

Predicting the Structures of Glycans, Glycoproteins, and Their Complexes

(2018) Robert J. Woods   CHEMICAL REVIEWS

The GAGOme: a cell-based library of displayed glycosaminoglycans

(2018) Yen-Hsi Chen et al.   NATURE METHODS

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Perspective on computational simulations of glycosaminoglycans

(2018) Balaji Nagarajan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview

(2018) Veronica Salmaso et al.   Frontiers in Pharmacology

Heparan sulfate as a regulator of inflammation and immunity

(2018) Laura E. Collins et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)

(2018) Michael Böhm et al.   NUCLEIC ACIDS RESEARCH

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

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

Reconfiguring the AR-TIF2 Protein–Protein Interaction HCS Assay in Prostate Cancer Cells and Characterizing the Hits from a LOPAC Screen

(2016) Ashley T. Fancher et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Shed proteoglycans in tumor stroma

(2016) Zoi Piperigkou et al.   CELL AND TISSUE RESEARCH

Heparin and anticoagulation

(2016) Robert J Linhardt   Frontiers in Bioscience-Landmark

Computational analysis of interactions in structurally available protein–glycosaminoglycan complexes

(2016) Sergey A Samsonov et al.   GLYCOBIOLOGY

Glycosaminoglycanomics: where we are

(2016) Sylvie Ricard-Blum et al.   GLYCOCONJUGATE JOURNAL

Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking

(2016) Anita K. Nivedha et al.   Journal of Chemical Theory and Computation

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Syndecan-1 increases B-lymphoid cell extravasation in response to HIV-1 Tat via αvβ3/pp60src/pp125FAK pathway

(2016) C Urbinati et al.   ONCOGENE

Angiogenic growth factors interactome and drug discovery: The contribution of surface plasmon resonance

(2015) Marco Rusnati et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Keratan sulfate: An up-to-date review

(2015) Vitor H. Pomin   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Biosynthesis of glycosaminoglycans: associated disorders and biochemical tests

(2015) Florin Sasarman et al.   JOURNAL OF INHERITED METABOLIC DISEASE

Determination of Substrate Specificities Against ��-Glucosidase A (BglA) from Thermotoga maritime: A Molecular Docking Approach

(2015) Muhammad Ibrahim Rajoka et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Proteoglycan form and function: A comprehensive nomenclature of proteoglycans

(2015) Renato V. Iozzo et al.   MATRIX BIOLOGY

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

(2015) Paola Chiodelli et al.   MOLECULES

The effect of water on the binding of glycosaminoglycan saccharides to hydroxyapatite surfaces: a molecular dynamics study

(2015) Sergio E. Ruiz Hernandez et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structure and Response to Flow of the Glycocalyx Layer

(2014) Eduardo R. Cruz-Chu et al.   BIOPHYSICAL JOURNAL

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

(2014) Nehru Viji Sankaranarayanan et al.   GLYCOBIOLOGY

Coarse-Grained Model of Glycosaminoglycans

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

Biosynthesis and function of chondroitin sulfate

(2013) Tadahisa Mikami et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Bridging the past and the future of virology: Surface plasmon resonance as a powerful tool to investigate virus/host interactions

(2013) Marco Rusnati et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Glycomics meets genomics, epigenomics and other high throughput omics for system biology studies

(2013) Vlatka Zoldoš et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Heparan sulfate proteoglycans in the control of B cell development and the pathogenesis of multiple myeloma

(2013) Rogier M. Reijmers et al.   FEBS Journal

Pathophysiology of heparan sulphate: many diseases, few drugs

(2013) U. Lindahl et al.   JOURNAL OF INTERNAL MEDICINE

The Nobel Prize in Chemistry 2013 for the Development of Multiscale Models of Complex Chemical Systems: A Tribute to Martin Karplus, Michael Levitt and Arieh Warshel

(2013) Hélène Hodak   JOURNAL OF MOLECULAR BIOLOGY

Mallard Blue: A High-Affinity Selective Heparin Sensor That Operates in Highly Competitive Media

(2013) Stephen M. Bromfield et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Software tools for identification, visualization and analysis of protein tunnels and channels

(2012) Jan Brezovsky et al.   BIOTECHNOLOGY ADVANCES

GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates

(2012) Laercio Pol-Fachin et al.   Journal of Chemical Theory and Computation

The “CPC Clip Motif”: A Conserved Structural Signature for Heparin-Binding Proteins

(2012) Marc Torrent et al.   PLoS One

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

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

Polysulfated/Sulfonated Compounds for the Development of Drugs at the Crossroad of Viral Infection and Oncogenesis

(2009) Marco Rusnati et al.   CURRENT PHARMACEUTICAL DESIGN

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

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

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Sulfated K5 Escherichia coli polysaccharide derivatives: A novel class of candidate antiviral microbicides

(2009) Marco Rusnati et al.   PHARMACOLOGY & THERAPEUTICS

Polyanionic Drugs and Viral Oncogenesis: a Novel Approach to Control Infection, Tumor-associated Inflammation and Angiogenesis

(2008) Chiara Urbinati et al.   MOLECULES

Domain motions of hyaluronan lyase underlying processive hyaluronan translocation

(2008) Harshad V. Joshi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS