An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data (Q30955555)

19 September 2017

An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data (English)

1 reference

cryogenic electron microscopy

19 September 2017

0 references

transmembrane protein

0 references

1 reference

Sarel J Fleishman

1

0 references

Nir Ben-Tal

object named as

Nir Ben-Tal

5

0 references

author name string

Susan Harrington

2

1 reference

19 September 2017

Richard A Friesner

3

1 reference

19 September 2017

Barry Honig

4

1 reference

19 September 2017

language of work or name

English

0 references

publication date

31 August 2004

1 reference

19 September 2017

1 reference

19 September 2017

87

1 reference

19 September 2017

3448-3459

1 reference

19 September 2017

5

1 reference

Raster3D: photorealistic molecular graphics

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Assigning transmembrane segments to helices in intermediate-resolution structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Structure and gating mechanism of the acetylcholine receptor pore

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A putative molecular-activation switch in the transmembrane domain of erbB2.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Transmembrane helix predictions revisited

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

An approach to membrane protein structure without crystals.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

The open pore conformation of potassium channels

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

The 3-D structure of microsomal glutathione transferase 1 at 6 A resolution as determined by electron crystallography of p22(1)2(1) crystals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Motifs of serine and threonine can drive association of transmembrane helices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Electron cryomicroscopy methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Substitution rates in alpha-helical transmembrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A new method to model membrane protein structure based on silent amino acid substitutions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Helical membrane proteins: diversity of functions in the context of simple architecture

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Bridging the information gap: computational tools for intermediate resolution structure interpretation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Helical membrane protein folding, stability, and evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Crystal structure of rhodopsin: A G protein-coupled receptor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Riding the wave: structural and energetic principles of helical membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

The GxxxG motif: a framework for transmembrane helix-helix association

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Membrane protein folding and stability: physical principles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

The packing density in proteins: standard radii and volumes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Three-dimensional structure of a recombinant gap junction membrane channel

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

TOXCAT: a measure of transmembrane helix association in a biological membrane

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Principles governing amino acid composition of integral membrane proteins: application to topology prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Principles of membrane protein assembly and structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A transmembrane helix dimer: structure and implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Structure, transmembrane topology and helix packing of P-type ion pumps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A method for alpha-helical integral membrane protein fold prediction.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Low resolution structure of bovine rhodopsin determined by electron cryo-microscopy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Stability of "salt bridges" in membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Analysis of membrane and surface protein sequences with the hydrophobic moment plot

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Hydrophobic organization of membrane proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A Cα Model for the Transmembrane α Helices of Gap Junction Intercellular Channels

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A simple method for modeling transmembrane helix oligomers

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Folding of bundles of alpha-helices in solution, membranes, and adsorbed overlayers.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Structure. Rhodopsin sees the light

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Are membrane proteins "inside-out" proteins?

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

A potential smoothing algorithm accurately predicts transmembrane helix packing.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Arrangement of rhodopsin transmembrane α-helices

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304811

Neu receptor dimerization

25 November 2018

1 reference

12 December 2020

Understanding membrane protein structure by design

1 reference

12 December 2020

Acetylcholine receptor channel imaged in the open state

1 reference

12 December 2020

Helix packing in membrane proteins

1 reference

12 December 2020

Structural clues in the sequences of the aquaporins

1 reference

12 December 2020

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

1 reference

12 December 2020

Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban

1 reference

12 December 2020

Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin

1 reference

12 December 2020

Membrane protein folding and oligomerization: the two-stage model

1 reference

12 December 2020

Modeling of transmembrane seven helix bundles

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.046417

Identifiers

DOI

1 reference

release_ydkyjz4evncdtjfnmvk5jjhoce

19 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ydkyjz4evncdtjfnmvk5jjhoce

24 November 2022

mapped directly with Wikidata item

1 reference

19 September 2017

1 reference