CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. (Q34085563)

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17 January 2020

title

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling (English)

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17 January 2020

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5

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17 January 2020

Alex MacKerell

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17 January 2020

author name string

Olgun Guvench

1

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17 January 2020

Sairam S Mallajosyula

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17 January 2020

E Prabhu Raman

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17 January 2020

Elizabeth Hatcher

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17 January 2020

Theresa J Foster

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17 January 2020

Francis W Jamison

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publication date

1 October 2011

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Journal of Chemical Theory and Computation

17 January 2020

published in

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17 January 2020

volume

7

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17 January 2020

issue

10

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17 January 2020

page(s)

3162-3180

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

17 January 2020

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

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CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

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5 July 2018

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Insights into the geometrical features underlying beta-O-GlcNAc glycosylation: water pockets drastically modulate the interactions between the carbohydrate and the peptide backbone

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Automated conformational energy fitting for force-field development.

5 July 2018

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Comparative protein structure modeling using Modeller

5 July 2018

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5 July 2018

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5 July 2018

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Serine versus threonine glycosylation: the methyl group causes a drastic alteration on the carbohydrate orientation and on the surrounding water shell

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Structures of the Cd44-hyaluronan complex provide insight into a fundamental carbohydrate-protein interaction

5 July 2018

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5 July 2018

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Effect of beta-O-glucosylation on L-Ser and L-Thr diamides: a bias toward alpha-helical conformations.

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

5 July 2018

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Data mining the protein data bank: automatic detection and assignment of carbohydrate structures

5 July 2018

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Regulatory roles of carbohydrate ligands for selectins in the homing of lymphocytes.

5 July 2018

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An improved OPLS-AA force field for carbohydrates

5 July 2018

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Addition of a single gp120 glycan confers increased binding to dendritic cell-specific ICAM-3-grabbing nonintegrin and neutralization escape to human immunodeficiency virus type 1.

5 July 2018

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Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds

5 July 2018

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The Cambridge Structural Database: a quarter of a million crystal structures and rising

5 July 2018

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5 July 2018

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The emerging significance of O-GlcNAc in cellular regulation

28 October 2018

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Solvent interactions determine carbohydrate conformation

5 July 2018

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5 July 2018

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Comparative protein structure modeling of genes and genomes

5 July 2018

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5 July 2018

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Antigen structure and genetic basis of histo-blood groups A, B and O: their changes associated with human cancer

5 July 2018

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Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

5 July 2018

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Canonical dynamics: Equilibrium phase-space distributions

5 July 2018

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Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies

5 July 2018

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Comparative protein modelling by satisfaction of spatial restraints

5 July 2018

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5 July 2018

Mucin-Type Glycoproteins

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A carbohydrate domain common to both sialyl Le(a) and sialyl Le(X) is recognized by the endothelial cell leukocyte adhesion molecule ELAM-1

5 July 2018

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Primary structural requirements for the enzymatic formation of the N-glycosidic bond in glycoproteins. Studies with natural and synthetic peptides

5 July 2018

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Mechanism of binding site conformational switching in the CD44-hyaluronan protein-carbohydrate binding interaction.

5 July 2018

1 reference

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Free energy landscapes of iduronic acid and related monosaccharides

28 October 2018

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

28 October 2018

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Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

28 October 2018

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A new GROMOS force field for hexopyranose-based carbohydrates

28 October 2018

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Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding.

28 October 2018

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Alcohols, ethers, carbohydrates, and related compounds. IV. Carbohydrates

28 October 2018

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Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

28 October 2018

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Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

28 October 2018

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Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes

28 October 2018

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Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

28 October 2018

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12 December 2020

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

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12 December 2020

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

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12 December 2020

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Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

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12 December 2020

Quantum Mechanical Analysis of 1,2-Ethanediol Conformational Energetics and Hydrogen Bonding

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12 December 2020

The Conformation of the Sialyl Lewis X Ligand Changes upon Binding to E-Selectin

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12 December 2020

Glycobiology: Toward Understanding the Function of Sugars

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12 December 2020

Computational studies on carbohydrates: in vacuo studies using a revised AMBER force field, AMB99C, designed for alpha-(1-->4) linkages

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12 December 2020

5 nanosecond molecular dynamics and NMR study of conformational transitions in the sialyl-Lewis X antigen

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12 December 2020

A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers

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12 December 2020

Identifiers

DOI

10.1021/CT200328P

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22125473%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22125473%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference