(Q36461179)

14 August 2017

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

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14 August 2017

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13

David A Case

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Wonpil Im

17

object named as

Wonpil Im

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14 August 2017

14

Charles L Brooks

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14 August 2017

12

Vijay S Pande

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14 August 2017

Jumin Lee

1

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14 August 2017

Xi Cheng

2

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14 August 2017

Jason M Swails

3

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14 August 2017

Min Sun Yeom

4

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14 August 2017

Peter K Eastman

5

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14 August 2017

Justin A Lemkul

6

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14 August 2017

Shuai Wei

7

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14 August 2017

Joshua Buckner

8

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14 August 2017

Jong Cheol Jeong

9

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14 August 2017

Yifei Qi

10

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14 August 2017

Sunhwan Jo

11

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14 August 2017

David A Case

13

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14 August 2017

Alexander D MacKerell

15

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14 August 2017

Jeffery B Klauda

16

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14 August 2017

3 December 2015

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Journal of Chemical Theory and Computation

14 August 2017

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14 August 2017

12

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14 August 2017

1

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14 August 2017

405-413

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describes a project that uses

14 August 2017

AMBER

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maintained by WikiProject

inferred from title

WikiProject Software

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cites work

An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Another Piece of the Membrane Puzzle: Extending Slipids Further

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Probing the importance of lipid diversity in cell membranes via molecular simulation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Computational characterization of structural dynamics underlying function in active membrane transporters

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

E. coli outer membrane and interactions with OmpLA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Lipid14: The Amber Lipid Force Field.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

The molecular structure of the liquid-ordered phase of lipid bilayers.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Molecular simulation approaches to membrane proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

CHARMM: the biomolecular simulation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Additive empirical force field for hexopyranose monosaccharides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Membrane lipids: where they are and how they behave

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Automated builder and database of protein/membrane complexes for molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Scalable molecular dynamics with NAMD

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

The Amber biomolecular simulation programs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Mechanism of the lamellar/inverse hexagonal phase transition examined by high resolution x-ray diffraction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Effect of chain length and unsaturation on elasticity of lipid bilayers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Canonical dynamics: Equilibrium phase-space distributions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Improving the CHARMM force field for polyunsaturated fatty acid chains.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Lipid organization of the plasma membrane

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Influence of ester-modified lipids on bilayer structure.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Update of the cholesterol force field parameters in CHARMM.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

Structure and lipid interaction of N-palmitoylsphingomyelin in bilayer membranes as revealed by 2H-NMR spectroscopy

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4712441

ST-analyzer: a web-based user interface for simulation trajectory analysis

21 September 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations

1 reference

12 December 2020

Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains

1 reference

12 December 2020

Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms

1 reference

12 December 2020

Membrane-binding mechanism of a peripheral membrane protein through microsecond molecular dynamics simulations

1 reference

12 December 2020

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

1 reference

12 December 2020

Identifiers

DOI

10.1021/ACS.JCTC.5B00935

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

26631602

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