(Q34085563)

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

17 January 2020

title

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

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

0 references

1 reference

5

1 reference

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17 January 2020

Alex MacKerell

8

1 reference

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17 January 2020

author name string

Olgun Guvench

1

1 reference

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17 January 2020

Sairam S Mallajosyula

2

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

E Prabhu Raman

3

1 reference

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17 January 2020

Elizabeth Hatcher

4

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

Theresa J Foster

6

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

Francis W Jamison

7

1 reference

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17 January 2020

publication date

1 October 2011

1 reference

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

Journal of Chemical Theory and Computation

17 January 2020

published in

1 reference

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17 January 2020

volume

7

1 reference

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17 January 2020

issue

10

1 reference

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17 January 2020

page(s)

3162-3180

1 reference

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

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

17 January 2020

cites work

1 reference

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Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids

5 July 2018

1 reference

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Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Glycans as receptors for influenza pathogenesis

5 July 2018

1 reference

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Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

5 July 2018

1 reference

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Consequences of the expression of sialylated antigens in breast cancer

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

A designed chimeric cyanovirin-N homolog lectin: Structure and molecular basis of sucrose binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

CHARMM: the biomolecular simulation program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Additive empirical force field for hexopyranose monosaccharides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Automated conformational energy fitting for force-field development.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Comparative protein structure modeling using Modeller

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Solvated ensemble averaging in the calculation of partial atomic charges

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

GLYCAM06: a generalizable biomolecular force field. Carbohydrates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

N-Acetylated amino sugars: the dependence of NMR 3J(HNH2)-couplings on conformation, dynamics and solvent

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Glycan-based interactions involving vertebrate sialic-acid-recognizing proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Glycoprotein structural genomics: solving the glycosylation problem

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Selectins and glycosyltransferases in leukocyte rolling in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Hyaluronan: the local solution conformation determined by NMR and computer modeling is close to a contracted left-handed 4-fold helix.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Scalable molecular dynamics with NAMD

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Selectin antagonists : therapeutic potential in asthma and COPD.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Empirical force fields for biological macromolecules: overview and issues.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Hyaluronan: from extracellular glue to pericellular cue.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Roles of N-linked glycans in the endoplasmic reticulum

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

An improved OPLS-AA force field for carbohydrates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

5 July 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

The emerging significance of O-GlcNAc in cellular regulation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Solvent interactions determine carbohydrate conformation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Modeling of loops in protein structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Comparative protein structure modeling of genes and genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Computational studies on carbohydrates: solvation studies on maltose and cyclomaltooligosaccharides (cyclodextrins) using a DFT/ab initio-derived empirical force field, AMB99C.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Canonical dynamics: Equilibrium phase-space distributions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Comparative protein modelling by satisfaction of spatial restraints

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

5 July 2018

Mucin-Type Glycoproteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

Free energy landscapes of iduronic acid and related monosaccharides

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

A new GROMOS force field for hexopyranose-based carbohydrates

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224046

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

28 October 2018

1 reference

12 December 2020

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

1 reference

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

1 reference

12 December 2020

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Glycobiology: Toward Understanding the Function of Sugars

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

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

1 reference

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

PubMed publication ID

22125473

1 reference