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Lipidbook specifications

Information


Unique identifier OMICS_08569
Name Lipidbook
Restrictions to use None
Content license CC Attribution
Maintained Yes

Maintainer


  • person_outline Oliver Beckstein

Publication for Lipidbook

Lipidbook citations

 (6)
library_books

Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers

2017
PLoS One
PMCID: 5695277
PMID: 29125878
DOI: 10.1371/journal.pone.0187216

[…] The initial coordinates for pardaxin were obtained from protein data bank (PDB ID: 1XC0)[]. The starting membrane coordinates of POPG were taken from Lipidbook [] and the initial coordinates and topologies of DMPC, DPPC, and POPC bilayers were obtained from the Tieleman laboratory []. The POPG/POPE mixed bilayers were taken from previous studies [, […]

library_books

Molecular dynamics exploration of poration and leaking caused by Kalata B1 in HIV infected cell membrane compared to host and HIV membranes

2017
Sci Rep
PMCID: 5472625
PMID: 28620219
DOI: 10.1038/s41598-017-03745-2

[…] uct all MD simulations in this study. The Martini force field, version 2.1– was used in the CG MD simulations, and GROMOS53a6 was used in the AA simulations. Lipid force fields were obtained from the Lipidbook database. The CG model of the IN membrane system at 100 µs in the second simulation condition was reverse-transformed to the AA models using the method developed by Wassenaar et al.. All MD […]

library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] gy function to describe the energy landscape of the system with respect to the relative coordinates of the constituent atoms, which represent the structure of the studied system . In this regard, the Lipidbook, a public database for force-field parameters used in simulating biological membrane systems , and the Course Grained Database (CGDB) can be useful. Significant progress has been made in th […]

call_split

Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights

2014
PMCID: 4242812
PMID: 25422503
DOI: 10.1085/jgp.201411219
call_split See protocol

[…] simulation packages (). All simulations used the OPLS-AA force field (; ; ) with the TIP4P water model () and OPLS-UA parameters for POPC lipids (; provided by M. Ulmschneider and available from the Lipidbook force field repository; see ). A POPC bilayer was studied as a generic model of a native-like membrane environment instead of other lipid compositions, as the POPC lipid parameters have been […]

library_books

Interactions of Lipids and Detergents with a Viral Ion Channel Protein: Molecular Dynamics Simulation Studies

2014
PMCID: 4306293
PMID: 25286030
DOI: 10.1021/jp505127y

[…] the His27 protonation state showed no significant differences in stability (Figure S12, ). CG and AT parameters for DHPC and DDM were as described those in ref () and available from LipidBook (http://lipidbook.bioch.ox.ac.uk/). Analyses were performed using GROMACS tools, MDAnalysis (mdanalysis.googlecode.com), and locally written code. Visualization used VMD. […]

library_books

On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics

2014
PLoS One
PMCID: 4139306
PMID: 25141217
DOI: 10.1371/journal.pone.0104778

[…] Table T1 both in . We specify the parameters used for each simulation in the section below. Input files used for the simulations are given in the supporting information and have been submitted to the Lipidbook website. Analysis of standard properties of the bilayers, such as area per lipid are given in . […]

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Lipidbook institution(s)
Department of Biochemistry, University of Oxford, Oxford, UK

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