Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment (Q37319674)

19 August 2017

Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment (English)

1 reference

19 August 2017

Eric L Peterson

1

1 reference

19 August 2017

Jané Kondev

series ordinal

2

1 reference

19 August 2017

Julie A Theriot

series ordinal

3

1 reference

19 August 2017

Rob Phillips

series ordinal

4

1 reference

19 August 2017

language of work or name

English

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publication date

7 April 2009

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19 August 2017

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19 August 2017

25

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19 August 2017

11

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19 August 2017

1356-1362

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Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Does common architecture reveal a viral lineage spanning all three domains of life?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

De novo proteins from designed combinatorial libraries

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Progress towards mapping the universe of protein folds

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

A cell-based screen for function of the four-helix bundle protein Rop: a new tool for combinatorial experiments in biophysics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Dictionary of recurrent domains in protein structures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

A designed four helix bundle protein with native-like structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Functional rapidly folding proteins from simplified amino acid sequences.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

An iterative method for extracting energy-like quantities from protein structures.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Protein structure comparison by alignment of distance matrices

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Fast databank searching with a reduced amino-acid alphabet

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Redesigning the hydrophobic core of a four-helix-bundle protein

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Identification of common molecular subsequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

The meaning and use of the area under a receiver operating characteristic (ROC) curve

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Theory for the folding and stability of globular proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

The relation between the divergence of sequence and structure in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Amino acid substitution matrices from protein blocks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Simplified amino acid alphabets based on deviation of conditional probability from random background.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Simplified amino acid alphabets for protein fold recognition and implications for folding.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

A computational approach to simplifying the protein folding alphabet.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732308

A Structural Basis for Sequence Comparisons

2 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP164

Emergence of Preferred Structures in a Simple Model of Protein Folding

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP164

Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

21 January 2018

1 reference

12 December 2020

Optimized representations and maximal information in proteins

1 reference

12 December 2020

Structure-derived substitution matrices for alignment of distantly related sequences

1 reference

12 December 2020

What is the Minimum Number of Letters Required to Fold a Protein?

1 reference

12 December 2020

Reduction of protein sequence complexity by residue grouping

1 reference

12 December 2020

10.1093/BIOINFORMATICS/BTP164

Identifiers

DOI

1 reference

journals/bioinformatics/PetersonKTP09

19 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

19 August 2017

PubMed publication ID

19351620

1 reference