Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools (Q26821837)

language of work or name

1 reference

2013

1 reference

Computational and Structural Biotechnology Journal

published in

1 reference

volume

5

1 reference

page(s)

e201302014

1 reference

CHARMM: the biomolecular simulation program

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

7 April 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Scalable molecular dynamics with NAMD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

VMD: visual molecular dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

The fluid mosaic model of the structure of cell membranes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

OPM database and PPM web server: resources for positioning of proteins in membranes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Lipid rafts as a membrane-organizing principle

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Databases in protein crystallography

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Setting up and running molecular dynamics simulations of membrane proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Sphingomyelin-cholesterol domains in phospholipid membranes: atomistic simulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Ligand Depot: a data warehouse for ligands bound to macromolecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Setting up and optimization of membrane protein simulations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Model for the structure of the lipid bilayer

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylceramide

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Liquid-ordered phase formation in cholesterol/sphingomyelin bilayers: all-atom molecular dynamics simulations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Molecular view of cholesterol flip-flop and chemical potential in different membrane environments.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

PACKMOL: a package for building initial configurations for molecular dynamics simulations.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Exploring the conformational space of Vpu from HIV-1: a versatile adaptable protein.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3962210

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

28 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/24688707

12 December 2020

inferred from PubMed ID database lookup

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer

1 reference

https://pubmed.ncbi.nlm.nih.gov/24688707

12 December 2020

inferred from PubMed ID database lookup

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.5936%2FCSBJ.201302014

7 January 2021

inferred from DOI database lookup

Two-dimensional packing problems: A survey

1 reference

https://api.crossref.org/works/10.5936%2FCSBJ.201302014

7 January 2021

inferred from DOI database lookup

Interaction of Surfactin with Membranes: A Computational Approach

1 reference

https://api.crossref.org/works/10.5936%2FCSBJ.201302014

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.5936/CSBJ.201302014

0 references

1 reference

PubMed publication ID

24688707

1 reference