TMKink: a method to predict transmembrane helix kinks (Q30402555)

16 October 2017

TMKink: a method to predict transmembrane helix kinks (English)

1 reference

16 October 2017

transmembrane protein

0 references

3

James U Bowie

1 reference

16 October 2017

Alejandro D Meruelo

1

1 reference

PMCID

3149198

16 October 2017

Ilan Samish

series ordinal

2

1 reference

16 October 2017

2 June 2011

1 reference

16 October 2017

1 reference

16 October 2017

20

1 reference

16 October 2017

7

1 reference

16 October 2017

1256-1264

1 reference

Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Internally bridging water molecule in transmembrane alpha-helical kink

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Prediction of membrane protein structures with complex topologies using limited constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

OPM: orientations of proteins in membranes database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Helical packing patterns in membrane and soluble proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Ser and Thr residues modulate the conformation of pro-kinked transmembrane alpha-helices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Multiple sequence alignment with the Clustal series of programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Matrix2png: a utility for visualizing matrix data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Beta2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Scoring residue conservation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

A protein sequence that can encode native structure by disfavoring alternate conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Non-alpha-helical elements modulate polytopic membrane protein architecture.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

The PSIPRED protein structure prediction server

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Prediction of protein secondary structure at better than 70% accuracy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Protein secondary structure prediction with a neural network

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149198

Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction

20 June 2018

1 reference

A simple method for modeling transmembrane helix oligomers

21 January 2018

1 reference

The glycophorin A transmembrane domain dimer: Sequence-specific propensity for a right-handed supercoil of helixes

21 January 2018

1 reference

Proline-induced distortions of transmembrane helices.

21 January 2018

1 reference

Prediction of protein supersecondary structures based on the artificial neural network method.

21 January 2018

1 reference

Computational design of peptides that target transmembrane helices.

21 January 2018

1 reference

Prokink: a protocol for numerical evaluation of helix distortions by proline.

21 January 2018

1 reference

Automatic early stopping using cross validation: quantifying the criteria

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21563225

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.653

1 reference

release_frq63skp5vfqtalqph3jcvk2i4

16 October 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/frq63skp5vfqtalqph3jcvk2i4

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

3149198

1 reference

16 October 2017

1 reference

PMCID

3149198