Computational modeling of membrane proteins (Q26995693)

main subject

computational biology

1 reference

1 reference

Jeffrey J. Gray

3

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author name string

Julia Koehler Leman

series ordinal

1

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Martin B. Ulmschneider

series ordinal

2

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language of work or name

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January 2015

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83

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page(s)

1-24

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issue

1

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Perspectives in magnetic resonance: NMR in the post-FFT era

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Activation and allosteric modulation of a muscarinic acetylcholine receptor

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Coarse-grain modelling of protein-protein interactions

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural and energetic basis of folded-protein transport by the FimD usher

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Three-dimensional structures of membrane proteins from genomic sequencing

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Transmembrane helix dimerization: beyond the search for sequence motifs

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

I-TASSER: a unified platform for automated protein structure and function prediction

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Principles of conduction and hydrophobic gating in K+ channels

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

NMR structure determination for larger proteins using backbone-only data

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

CHARMM: the biomolecular simulation program

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

GeNMR: a web server for rapid NMR-based protein structure determination

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

I-TASSER server for protein 3D structure prediction

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

X-ray structure of a voltage-dependent K+ channel

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Architecture of the large subunit of the mammalian mitochondrial ribosome

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structure of the SecY channel during initiation of protein translocation

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A Structural Study of Ion Permeation in OmpF Porin from Anomalous X-ray Diffraction and Molecular Dynamics Simulations

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Subangstrom Resolution X-Ray Structure Details Aquaporin-Water Interactions

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crystal structure of the entire respiratory complex I

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structure of a presenilin family intramembrane aspartate protease

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The Binding of Antibiotics in OmpF Porin

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Principles for designing ideal protein structures

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Facile backbone structure determination of human membrane proteins by NMR spectroscopy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Solution NMR Structure of Proteorhodopsin

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G Proteins, PIP2, and Sodium

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A transient and low-populated protein-folding intermediate at atomic resolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Solution Nuclear Magnetic Resonance Structure of Membrane-Integral Diacylglycerol Kinase

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structure of the human voltage-dependent anion channel

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crystal structure of a Kir3.1-prokaryotic Kir channel chimera

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crystal structure of the potassium channel KirBac1.1 in the closed state

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crystal structure and mechanism of a calcium-gated potassium channel

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Scalable molecular dynamics with NAMD

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

GROMACS: fast, flexible, and free

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Protein secondary structure prediction based on position-specific scoring matrices

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A simple method for displaying the hydropathic character of a protein

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

International Union of Pharmacology. XLI. Compendium of voltage-gated ion channels: potassium channels

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The versatile beta-barrel membrane protein

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Protein structure prediction and structural genomics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Effective energy function for proteins in solution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural characterization and mutational assessment of podocin - a novel drug target to nephrotic syndrome - an in silico approach

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crystal structure of a mammalian voltage-dependent Shaker family K+ channel

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Combining prediction of secondary structure and solvent accessibility in proteins

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Protein homology detection by HMM-HMM comparison

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Cross-link guided molecular modeling with ROSETTA

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

GOMoDo: A GPCRs online modeling and docking webserver

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Systematic validation of protein force fields against experimental data

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

MeMotif: a database of linear motifs in alpha-helical transmembrane proteins

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

TOPDB: topology data bank of transmembrane proteins

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The Jpred 3 secondary structure prediction server

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Development and testing of a general amber force field

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

GPU-accelerated molecular modeling coming of age

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Comparative protein structure modeling using MODELLER

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Crucial role of perfringolysin O D1 domain in orchestrating structural transitions leading to membrane-perforating pores: a hydrogen-deuterium exchange study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Tethered protein display identifies a novel Kir3.2 (GIRK2) regulator from protein scaffold libraries

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Identification of specific ligand-receptor interactions that govern binding and cooperativity of diverse modulators to a common metabotropic glutamate receptor 5 allosteric site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A mass spectrometry-based hybrid method for structural modeling of protein complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Rebuilding a macromolecular membrane complex at the atomic scale: case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

hERG potassium channel blockage by scorpion toxin BmKKx2 enhances erythroid differentiation of human leukemia cells K562

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Ionic channels as targets for drug design: a review on computational methods

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

BCL::Fold--protein topology determination from limited NMR restraints.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Modeling the conformational changes underlying channel opening in CFTR

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Embedding Aβ42 in heterogeneous membranes depends on cholesterol asymmetries

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Transmembrane protein alignment and fold recognition based on predicted topology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Biomolecular membrane protein crystallization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A computationally designed water-soluble variant of a G-protein-coupled receptor: the human mu opioid receptor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Charge asymmetry in the proteins of the outer membrane.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

BCL::MP-fold: folding membrane proteins through assembly of transmembrane helices

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Memoir: template-based structure prediction for 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=4270820

Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Conformational states of melittin at a bilayer interface

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Computer simulations of lipid membrane domains.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Influence of lipids on protein-mediated transmembrane transport.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and 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=4270820

Coordinating the impact of structural genomics on the human α-helical transmembrane proteome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The dynamic process of β(2)-adrenergic receptor activation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The GPCR Network: a large-scale collaboration to determine human GPCR structure and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Membrane protein native state discrimination by implicit membrane models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Folding of outer 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=4270820

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Gain-of-function analogues of the pore-forming peptide melittin selected by orthogonal high-throughput screening.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Accurate protein structure modeling using sparse NMR data and homologous structure information

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural genomics plucks high-hanging 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=4270820

A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel 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=4270820

Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

BOCTOPUS: improved topology prediction of transmembrane β barrel 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=4270820

Predicting three-dimensional structures of transmembrane domains of β-barrel 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=4270820

Interactions between ionizable amino acid side chains at a lipid bilayer-water interface

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Tolerance to changes in membrane lipid composition as a selected trait 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=4270820

An introduction to 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=4270820

Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

TMKink: a method to predict transmembrane helix kinks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Optimal mutation sites for PRE data collection and membrane protein structure prediction.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Free-energy cost for translocon-assisted insertion 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=4270820

Challenges in protein folding simulations: Timescale, representation, and analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

RosettaEPR: an integrated tool for protein structure determination from sparse EPR data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Energy landscapes as a tool to integrate GPCR structure, dynamics, and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

MEDELLER: homology-based coordinate generation for 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=4270820

Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Amphiphile regulation of ion channel function by changes in the bilayer spring constant.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Amphipols, nanodiscs, and fluorinated surfactants: three nonconventional approaches to studying membrane proteins in aqueous solutions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Target promiscuity and heterogeneous effects of tarantula venom peptides affecting Na+ and K+ ion channels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

From the gating charge response to pore domain movement: initial motions of Kv1.2 dynamics under physiological voltage changes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Predicting protein-protein binding sites in 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=4270820

A QSAR study on some series of sodium and potassium channel blockers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A generic method for assignment of reliability scores applied to solvent accessibility predictions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Fast and accurate automatic structure prediction with HHpred.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Refinement of protein structures into low-resolution density maps using rosetta

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Interaction and conformational dynamics of membrane-spanning protein helices

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Transmembrane protein topology prediction using support vector machines

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Broad-spectrum antimicrobial peptides by rational combinatorial design and high-throughput screening: the importance of interfacial activity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Prediction of membrane protein structures with complex topologies using limited constraints

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A unified hydrophobicity scale for multispan 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=4270820

Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Protein-protein interactions in the membrane: sequence, structural, and biological motifs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

TOPDOM: database of domains and motifs with conservative location in transmembrane 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=4270820

De novo high-resolution protein structure determination from sparse spin-labeling EPR data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

On the origin of lipid asymmetry: the flip side of ion transport

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Toward high-resolution prediction and design of transmembrane helical protein structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Prediction of the burial status of transmembrane residues of helical 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=4270820

Scoring function accuracy for membrane protein structure prediction.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Protein structure prediction: combining de novo modeling with sparse experimental data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The interaction of spider gating modifier peptides with voltage-gated potassium channels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Helix-packing motifs in 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=4270820

Performance of cryogenic probes as a function of ionic strength and sample tube geometry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Lipid asymmetry of the eukaryotic plasma membrane: functions and related enzymes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

PROFtmb: a web server for predicting bacterial transmembrane beta barrel 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=4270820

Solution NMR of membrane proteins: practice and challenges

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A limited universe of membrane protein families and folds

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Prediction of transmembrane helix orientation in polytopic 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=4270820

Predicting the solvent accessibility of transmembrane residues from protein sequence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

On the accuracy of homology modeling and sequence alignment methods applied to 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=4270820

hERG potassium channels and cardiac arrhythmia

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Optimal isotope labelling for NMR protein structure determinations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Multipass membrane protein structure prediction using Rosetta

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Interfacial folding and membrane insertion of designed peptides studied by 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=4270820

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=4270820

Rapid protein fold determination using unassigned NMR data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Coupled prediction of protein secondary and tertiary structure

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Sequence motifs, polar interactions and conformational changes in helical 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=4270820

Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A microscopic view of ion conduction through the K+ channel.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The PredictProtein server.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Prediction of structure and function of G protein-coupled receptors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Modeling the 3D structure of GPCRs from sequence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Comparing function and structure between entire proteomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

De novo protein structure determination using sparse NMR data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Molecular dynamics of the KcsA K(+) channel in a bilayer membrane

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Do transmembrane protein superfolds exist?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Disposition of amphiphilic helices in heteropolar environments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Evaluation of current techniques for ab initio protein structure prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Overexpression of integral membrane proteins for structural studies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

The helical hydrophobic moment: a measure of the amphiphilicity of a helix

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Amino acid side-chain partition energies and distribution of residues in soluble 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=4270820

Identifying nonpolar transbilayer helices in amino acid sequences 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=4270820

Sequence specificity in the dimerization of transmembrane alpha-helices

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Surface and inside volumes in globular 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=4270820

Flexible gates generate occluded intermediates in the transport cycle of LacY.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Simultaneous prediction of protein secondary structure and transmembrane spans

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Benchmarking ligand-based virtual High-Throughput Screening with the PubChem database

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Modeling of open, closed, and open-inactivated states of the hERG1 channel: structural mechanisms of the state-dependent drug binding.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Mechanism of voltage gating in potassium channels

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Ab initio protein modeling into CryoEM density maps using EM-Fold

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Binding of perforin to membranes is sensitive to lipid spacing and not headgroup

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Molecular code for transmembrane-helix recognition by the Sec61 translocon

31 May 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

HELIQUEST: a web server to screen sequences with specific alpha-helical properties.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

PRIMSIPLR: prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

PREDDIMER: a web server for prediction of transmembrane helical dimers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

MP-T: improving membrane protein alignment for structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Prediction of the human membrane proteome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Effective energy function for proteins in lipid membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Brownian dynamics study of an open-state KcsA potassium channel.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Pharmacophore-based search, synthesis, and biological evaluation of anthranilic amides as novel blockers of the Kv1.5 channel

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Interacting sites of scorpion toxin ErgTx1 with hERG1 K+ channels.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Modeling ensembles of transmembrane beta-barrel proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

MONSSTER: a method for folding globular proteins with a small number of distance restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Calculations of pH-dependent binding of proteins to biological membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Model quality assessment for membrane proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Membrane perturbation by carbon nanotube insertion: pathways to internalization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Computer simulation study of fullerene translocation through lipid membranes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Update of the cholesterol force field parameters in CHARMM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Anton, a special-purpose machine for molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Engineering de novo membrane-mediated protein-protein communication networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Computational design of peptides that target transmembrane helices.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Detecting substrates bound to the secondary multidrug efflux pump EmrE by DNP-enhanced solid-state NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

A Novel Scoring Function for Predicting the Conformations of Tightly Packed Pairs of Transmembrane α-Helices

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

ExTopoDB: a database of experimentally derived topological models of transmembrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Sampling large conformational transitions: adenylate kinase as a testing ground

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

A web-based program (WHAT) for the simultaneous prediction of hydropathy, amphipathicity, secondary structure and transmembrane topology for a single protein sequence.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

Third generation prediction of secondary structures.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4270820

A novel structure-based virtual screening model for the hERG channel blockers

28 November 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24703

Improved segmental isotope labeling of proteins and application to a larger protein

21 January 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

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

1 reference

12 December 2020

Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides

1 reference

12 December 2020

Simulation of polyethylene glycol and calcium-mediated membrane fusion

1 reference

12 December 2020

United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.24703

1 reference

3347498

3347498

1 reference

1 reference

1 reference