Perspective on computational simulations of glycosaminoglycans

Controlled Chemoenzymatic Synthesis of Heparan Sulfate Oligosaccharides

(2018) Weigang Lu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Fluorous-tag assisted synthesis of a glycosaminoglycan mimetic tetrasaccharide as a high-affinity FGF-2 and midkine ligand

(2018) Susana Maza et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Using structurally defined oligosaccharides to understand the interactions between proteins and heparan sulfate

(2018) Ding Xu et al.   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

Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation

(2017) Cathy Ng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules

(2017) Balaji Nagarajan et al.   PLoS One

Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans

(2016) Arunima Singh et al.   CANADIAN JOURNAL OF CHEMISTRY

Chemical Synthesis of Glycosaminoglycans

(2016) Marco Mende et al.   CHEMICAL REVIEWS

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

(2016) Aurijit Sarkar et al.   GLYCOBIOLOGY

Biological roles of glycans

(2016) Ajit Varki   GLYCOBIOLOGY

Glycosaminoglycanomics: where we are

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

Molecular Basis of Chemokine CXCL5-Glycosaminoglycan Interactions

(2016) Krishna Mohan Sepuru et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Heparan sulfate hexasaccharide selectively inhibits cancer stem cells self-renewal by activating p38 MAP kinase

(2016) Nirmita J. Patel et al.   Oncotarget

The Cambridge Structural Database

(2016) Colin R. Groom et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Uncovering the Relationship between Sulphation Patterns and Conformation of Iduronic Acid in Heparan Sulphate

(2016) Po-Hung Hsieh et al.   Scientific Reports

Proteoglycans and Their Heterogeneous Glycosaminoglycans at the Atomic Scale

(2015) Benedict M. Sattelle et al.   BIOMACROMOLECULES

Re-visiting the structure of heparin

(2015) Benito Casu et al.   CARBOHYDRATE RESEARCH

Keratan sulfate: An up-to-date review

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

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Revision of the GROMOS 56A6CARBOforce field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

(2015) Wojciech Plazinski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Solution Structure of Heparin Pentasaccharide: NMR and DFT Analysis

(2015) Miloš Hricovíni   JOURNAL OF PHYSICAL CHEMISTRY B

Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides

(2015) Christina E. Faller et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Effect of Glycosaminoglycans (GAGs) on Amyloid Aggregation and Toxicity

(2015) Clara Iannuzzi et al.   MOLECULES

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

BFMP: A Method for Discretizing and Visualizing Pyranose Conformations

(2014) Spandana Makeneni et al.   Journal of Chemical Information and Modeling

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

Coarse-Grained Model of Glycosaminoglycans in Aqueous Salt Solutions. A Field-Theoretical Approach

(2014) Andrei L. Kolesnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Glycosaminoglycan Monosaccharide Blocks Analysis by Quantum Mechanics, Molecular Dynamics, and Nuclear Magnetic Resonance

(2014) Sergey A. Samsonov et al.   Biomed Research International

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

(2013) Benedict M. Sattelle et al.   BIOMACROMOLECULES

Synthesis of a Targeted Library of Heparan Sulfate Hexa- to Dodecasaccharides as Inhibitors of β-Secretase: Potential Therapeutics for Alzheimer’s Disease

(2013) Ralf Schwörer et al.   CHEMISTRY-A EUROPEAN JOURNAL

Synthetic probes of glycosaminoglycan function

(2013) Matthew E Griffin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Conformations of the iduronate ring in short heparin fragments described by time-averaged distance restrained molecular dynamics

(2013) J. C. Munoz-Garcia et al.   GLYCOBIOLOGY

Chemoenzymatic synthesis of glycosaminoglycans: Re-creating, re-modeling and re-designing nature's longest or most complex carbohydrate chains

(2013) P. L. DeAngelis et al.   GLYCOBIOLOGY

Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences

(2013) Art D. Bochevarov et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Toward an Accurate Conformational Modeling of Iduronic Acid

(2013) Pavel Oborský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydroxyl-Proton Hydrogen Bonding in the Heparin Oligosaccharide Arixtra in Aqueous Solution

(2013) Consuelo N. Beecher et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thrombin inhibition by the serpins

(2013) J. A. Huntington   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

3D structure of a heparin mimetic analogue of a FGF-1 activator. A NMR and molecular modelling study

(2013) Juan C. Muñoz-García et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

The power of coarse graining in biomolecular simulations

(2013) Helgi I. Ingólfsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism

(2012) W. Li et al.   BLOOD

Effect of the Substituents of the Neighboring Ring in the Conformational Equilibrium of Iduronate in Heparin-like Trisaccharides

(2012) Juan Carlos Muñoz-García et al.   CHEMISTRY-A EUROPEAN JOURNAL

Sulfamate proton solvent exchange in heparin oligosaccharides: Evidence for a persistent hydrogen bond in the antithrombin-binding pentasaccharide Arixtra

(2012) Derek J Langeslay et al.   GLYCOBIOLOGY

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

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

Dependence of Pyranose Ring Puckering on Anomeric Configuration: Methyl Idopyranosides

(2012) Benedict M. Sattelle et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational flexibility of a protein–carbohydrate complex and the structure and ordering of surrounding water

(2012) Madhurima Jana et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An overview of the Amber biomolecular simulation package

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

Is N-acetyl-d-glucosamine a rigid 4C1 chair?

(2011) Benedict M Sattelle et al.   GLYCOBIOLOGY

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

(2011) Nicolas Sapay et al.   GLYCOBIOLOGY

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils

(2011) Goundla Srinivas et al.   Journal of Chemical Theory and Computation

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

Solvation properties of N-acetyl-β-glucosamine: Molecular dynamics study incorporating electrostatic polarization

(2011) Yang Zhong et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

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

Synthesis of 3-O-sulfonated heparan sulfate octasaccharides that inhibit the herpes simplex virus type 1 host–cell interaction

(2011) Yu-Peng Hu et al.   Nature Chemistry

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

(2011) Enguerran Vanquelef et al.   NUCLEIC ACIDS RESEARCH

Chemoenzymatic Synthesis of Homogeneous Ultralow Molecular Weight Heparins

(2011) Y. Xu et al.   SCIENCE

Carbohydrate force fields

(2011) B. Lachele Foley et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

(2010) E. Autieri et al.   JOURNAL OF CHEMICAL PHYSICS

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

(2010) Volodymyr Babin et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Free Energy Landscapes of Iduronic Acid and Related Monosaccharides

(2010) Benedict M. Sattelle et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

GlycomeDB--a unified database for carbohydrate structures

(2010) R. Ranzinger et al.   NUCLEIC ACIDS RESEARCH

Modelling of β-d-glucopyranose ring distortion in different force fields: a metadynamics study

(2009) Vojtěch Spiwok et al.   CARBOHYDRATE RESEARCH

Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

(2009) Neha S. Gandhi et al.   CARBOHYDRATE RESEARCH

Martini Coarse-Grained Force Field: Extension to Carbohydrates

(2009) Cesar A. López et al.   Journal of Chemical Theory and Computation

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

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

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

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure, Receptor Binding, and Antigenicity of Influenza Virus Hemagglutinins from the 1957 H2N2 Pandemic

(2009) R. Xu et al.   JOURNAL OF VIROLOGY

The Basic Science of Articular Cartilage: Structure, Composition, and Function

(2009) Alice J. Sophia Fox et al.   Sports Health-A Multidisciplinary Approach

Depiction of the forces participating in the 2-O-sulfo-α-l-iduronic acid conformational preference in heparin sequences in aqueous solutions

(2008) Laercio Pol-Fachin et al.   CARBOHYDRATE RESEARCH

Contribution of glycosaminoglycans to viscoelastic tensile behavior of human ligament

(2008) Trevor J. Lujan et al.   JOURNAL OF APPLIED PHYSIOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural Studies of Heparan Sulfate Hexasaccharides: New Insights into Iduronate Conformational Behavior

(2008) Kevin J. Murphy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex

(2008) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra

(2008) Laurent Maveyraud et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS