(Q42037742)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

title

A generalized born implicit-membrane representation compared to experimental insertion free energies (English)

1 reference

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24 December 2019

3

1 reference

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24 December 2019

author name string

Martin B Ulmschneider

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

Jakob P Ulmschneider

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

Alfredo Di Nola

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

language of work or name

English

0 references

publication date

11 January 2007

1 reference

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24 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

volume

92

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

page(s)

2338-2349

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations

24 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Towards genome-scale structure prediction for transmembrane proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structure modeling of all identified G protein-coupled receptors in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Recognition of transmembrane helices by the endoplasmic reticulum translocon.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Understanding the energetics of helical peptide orientation in membranes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Peptides and proteins in membranes: what can we learn via computer simulations?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Membrane protein simulations: ion channels and bacterial outer membrane proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Synthetic peptides as models for intrinsic membrane proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Membrane protein folding: beyond the two stage model.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring (Review)

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Absolute comparison of simulated and experimental protein-folding dynamics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Impact of single-residue mutations on the structure and function of ovispirin/novispirin antimicrobial peptides

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structural basis of water-specific transport through the AQP1 water channel

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

A Monte Carlo study of peptide insertion into lipid bilayers: equilibrium conformations and insertion mechanisms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structure of the transmembrane region of the M2 protein H+ channel

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Orientation and dynamics of an antimicrobial peptide in the lipid bilayer by solid-state NMR spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

X-ray structure of sensory rhodopsin II at 2.1-A resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

In silico research in drug discovery

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Generalized born models of macromolecular solvation effects

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Role of the hinge region and the tryptophan residue in the synthetic antimicrobial peptides, cecropin A(1-8)-magainin 2(1-12) and its analogues, on their antibiotic activities and structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Association entropy in adsorption processes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Membrane simulations: bigger and better?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Orientation of cecropin A helices in phospholipid bilayers determined by solid-state NMR spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Interactions of alpha-helices with lipid bilayers: a review of simulation studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

The preference of tryptophan for membrane interfaces.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Do transmembrane protein superfolds exist?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

A transmembrane helix dimer: structure and implications

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Experimentally determined hydrophobicity scale for proteins at membrane interfaces

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Free-energy determinants of alpha-helix insertion into lipid bilayers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Three-dimensional solid-state NMR spectroscopy of a peptide oriented in membrane bilayers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structure and orientation of the antibiotic peptide magainin in membranes by solid-state nuclear magnetic resonance spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Overexpression of integral membrane proteins for structural studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Binding and action of cecropin and cecropin analogues: antibacterial peptides from insects.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. II. "Composition-space" refinement method

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Properties of integral membrane protein structures: derivation of an implicit membrane potential.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Membrane insertion of a potassium-channel voltage sensor

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Implicit solvent model estimates of the stability of model structures of the alamethicin channel

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Effective energy function for proteins in lipid membranes

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Energy of an Ion crossing a Low Dielectric Membrane: Solutions to Four Relevant Electrostatic Problems

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1864825

Structure determination of membrane proteins by NMR spectroscopy

3 November 2018

1 reference

12 December 2020

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer

1 reference

12 December 2020

Dipole lattice membrane model for protein calculations

1 reference

12 December 2020

Membrane protein folding and oligomerization: the two-stage model

1 reference

12 December 2020

Structure and orientation of the mammalian antibacterial peptide cecropin P1 within phospholipid membranes

1 reference

12 December 2020

Stop-transfer function of pseudo-random amino acid segments during translocation across prokaryotic and eukaryotic membranes

1 reference

12 December 2020

Molecular dynamics study of peptides in implicit water: ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.081810

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17218457%20AND%20SRC:MED&resulttype=core&format=json

24 December 2019

PubMed publication ID

17218457

1 reference