(Q30414402)

10 August 2017

β-sheet topology prediction with high precision and recall for β and mixed α/β proteins (English)

1 reference

10 August 2017

Christodoulos Floudas

series ordinal

2

object named as

Christodoulos A Floudas

0 references

author name string

Ashwin Subramani

series ordinal

1

1 reference

PMC publication ID

3302896

10 August 2017

language of work or name

English

0 references

publication date

9 March 2012

1 reference

10 August 2017

1 reference

10 August 2017

7

1 reference

10 August 2017

3

1 reference

10 August 2017

e32461

1 reference

Creative Commons Attribution 4.0 International

10 August 2017

start time

9 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other 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=3302896

A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

An improved hybrid global optimization method for protein tertiary structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Selecting high quality protein structures from diverse conformational ensembles.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Protein structure prediction and model quality assessment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Improving strand pairing prediction through exploring folding cooperativity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative 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=3302896

Progress and challenges in protein structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Protein folding by zipping and assembly

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Computational methods in protein structure prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Strict rules determine arrangements of strands in sandwich 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=3302896

A geometric construction determines all permissible strand arrangements of sandwich 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=3302896

Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Protein folding: the stepwise assembly of foldon units

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Common features in structures and sequences of sandwich-like 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=3302896

Distributions of beta sheets in proteins with application to structure prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Recursive domains in 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=3302896

Protein folding: from the levinthal paradox to structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Is protein folding hierarchic? II. Folding intermediates and transition states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Is protein folding hierarchic? I. Local structure and peptide folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in 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=3302896

Torsion angle dynamics for NMR structure calculation with the new program DYANA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

PROMOTIF--a program to identify and analyze structural motifs in 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=3302896

Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

The Greek key motif: extraction, classification and analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Identification and classification of protein fold families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Alpha plus beta folds revisited: some favoured motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

SCOP: a structural classification of proteins database for the investigation of sequences and structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Cooperativity in protein-folding kinetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

The anatomy and taxonomy of protein structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Folding units in globular 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=3302896

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=3302896

The classification and origins of protein folding patterns

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Hydrogen bonding in globular 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=3302896

A database of protein structure families with common folding motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

On the conformation of proteins: an analysis of beta-pleated sheets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Hierarchic organization of domains in globular 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=3302896

β-Sheet topology and the relatedness of 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=3302896

Handedness of crossover connections in beta sheets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

LINUS: a hierarchic procedure to predict the fold of a protein.

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032461

Prediction of beta-sheet topology and disulfide bridges in polypeptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032461

Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032461

Bayesian models and algorithms for protein β-sheet prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032461

Re-evaluating the "rules" of protein topology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032461

Beta-sheet prediction using inter-strand residue pairs and refinement with Hopfield neural network.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Predicting location and structure of beta-sheet regions using stochastic tree grammars.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3302896

Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22427840

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0032461

1 reference

10 August 2017

0 references

1 reference

PMC publication ID

3302896

10 August 2017

PubMed publication ID

22427840

1 reference

PMC publication ID

3302896