Preferred conformations ofN-glycan core pentasaccharide in solution and in glycoproteins

Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study

(2015) Hui Sun Lee et al.   Scientific Reports

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

(2014) Dhilon S. Patel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

(2013) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Quantification of Drive-Response Relationships Between Residues During Protein Folding

(2013) Yifei Qi et al.   Journal of Chemical Theory and Computation

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

(2013) Sunhwan Jo et al.   PLoS Computational Biology

Structure, mechanism and inhibition of Golgi α-mannosidase II

(2012) David R Rose   CURRENT OPINION IN STRUCTURAL BIOLOGY

Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution

(2012) Wataru Nishima et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Specific and Nonspecific Effects of Glycosylation

(2012) Christopher R. Ellis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanical Compressibility of the Glycosylphosphatidylinositol (GPI) Anchor Backbone Governed by Independent Glycosidic Linkages

(2012) Marko Wehle et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Glycan fragment database: a database of PDB-based glycan 3D structures

(2012) Sunhwan Jo et al.   NUCLEIC ACIDS RESEARCH

Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation

(2011) Suyong Re et al.   BIOPHYSICAL JOURNAL

Mechanisms and principles of N-linked protein glycosylation

(2011) Flavio Schwarz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins

(2011) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

(2011) Jason S. McLellan et al.   NATURE

Unique carbohydrate-carbohydrate interactions are required for high affinity binding between Fc RIII and antibodies lacking core fucose

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

Protein Native-State Stabilization by Placing Aromatic Side Chains in N-Glycosylated Reverse Turns

(2011) E. K. Culyba et al.   SCIENCE

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling

(2010) Lovorka Perić-Hassler et al.   CARBOHYDRATE RESEARCH

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects

(2010) Elisa Fadda et al.   DRUG DISCOVERY TODAY

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation

(2010) M. M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis and validation of carbohydrate three-dimensional structures

(2009) Thomas Lütteke   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Extracting the Causality of Correlated Motions from Molecular Dynamics Simulations

(2009) Hiqmet Kamberaj et al.   BIOPHYSICAL JOURNAL

Glycoprotein folding, quality control and ER-associated degradation

(2009) Gerardo Z Lederkremer   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

NMR Structure Determination of a Segmentally Labeled Glycoprotein Using in Vitro Glycosylation

(2009) Vadim Slynko et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The core trisaccharide of an N-linked glycoprotein intrinsically accelerates folding and enhances stability

(2009) S. R. Hanson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N-glycan structures: recognition and processing in the ER

(2009) Markus Aebi et al.   TRENDS IN BIOCHEMICAL SCIENCES

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

A simple and fast algorithm for K-medoids clustering

(2008) Hae-Sang Park et al.   EXPERT SYSTEMS WITH APPLICATIONS

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

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

Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

(2008) Amanda M. Salisburg et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing the Substrate Specificity of Golgi α-Mannosidase II by Use of Synthetic Oligosaccharides and a Catalytic Nucleophile Mutant

(2008) Wei Zhong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure of an O-GlcNAc transferase homolog provides insight into intracellular glycosylation

(2008) Carlos Martinez-Fleites et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Golgi  -mannosidase II cleaves two sugars sequentially in the same catalytic site

(2008) N. Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA