An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. (Q35034131)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24204234%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

title

An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis (English)

1 reference

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Mycobacterium tuberculosis

29 February 2020

main subject

protein design

0 references

0 references

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1

1 reference

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29 February 2020

Jeffrey Brender

3

1 reference

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29 February 2020

Jeff Czajka

4

1 reference

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29 February 2020

author name string

David Shultis

2

1 reference

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29 February 2020

David Marsh

5

1 reference

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29 February 2020

Felicia Gray

6

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29 February 2020

Tomasz Cierpicki

7

1 reference

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29 February 2020

Yang Zhang

8

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29 February 2020

publication date

24 October 2013

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PLOS Computational Biology

29 February 2020

published in

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29 February 2020

volume

9

1 reference

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29 February 2020

issue

10

1 reference

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29 February 2020

page(s)

e1003298

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Creative Commons Attribution 4.0 International

29 February 2020

copyright license

start time

24 October 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework.

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8 July 2018

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Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design

8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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Optimization by Simulated Annealing

8 July 2018

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8 July 2018

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8 July 2018

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IPRO: an iterative computational protein library redesign and optimization procedure

8 July 2018

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On the origin and highly likely completeness of single-domain protein structures.

8 July 2018

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8 July 2018

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Prediction of solvent accessibility and sites of deleterious mutations from protein sequence.

8 July 2018

1 reference

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TM-align: a protein structure alignment algorithm based on the TM-score

8 July 2018

1 reference

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Recapitulation of protein family divergence using flexible backbone protein design

8 July 2018

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The protein structure prediction problem could be solved using the current PDB library

8 July 2018

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Protein homology detection by HMM-HMM comparison

8 July 2018

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Scoring function for automated assessment of protein structure template quality

8 July 2018

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Theory of protein folding

8 July 2018

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The Pfam protein families database

8 July 2018

1 reference

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

8 July 2018

1 reference

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Solution structure of ade novoprotein from a designed combinatorial library

8 July 2018

1 reference

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A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins

8 July 2018

1 reference

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PISCES: a protein sequence culling server

8 July 2018

1 reference

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Designed to be stable: crystal structure of a consensus ankyrin repeat protein

8 July 2018

1 reference

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Structure of a de novo designed protein model of radical enzymes

8 July 2018

1 reference

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Further development and validation of empirical scoring functions for structure-based binding affinity prediction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3812052

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

8 July 2018

1 reference

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Native protein sequences are close to optimal for their structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3812052

De novo protein design. I. In search of stability and specificity.

8 July 2018

1 reference

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Protein secondary structure prediction based on position-specific scoring matrices

8 July 2018

1 reference

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Analyzing protein circular dichroism spectra for accurate secondary structures.

8 July 2018

1 reference

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Solution structure and dynamics of a de novo designed three-helix bundle protein

8 July 2018

1 reference

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High-resolution protein design with backbone freedom

8 July 2018

1 reference

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Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

8 July 2018

1 reference

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De novo protein design: fully automated sequence selection

8 July 2018

1 reference

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

8 July 2018

1 reference

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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

8 July 2018

1 reference

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Knowledge-based protein secondary structure assignment

8 July 2018

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

8 July 2018

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Profile analysis: detection of distantly related proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3812052

Conformational properties of alpha-synuclein in its free and lipid-associated states

8 July 2018

1 reference

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Estimation of globular protein secondary structure from circular dichroism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003298

Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003298

Determination of the folding of proteins as a function of denaturants, osmolytes or ligands using circular dichroism

21 January 2018

1 reference

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Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003298

Computer-aided design of a PDZ domain to recognize new target sequences.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3812052

Conserved residues and the mechanism of protein folding

25 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003298

Computational de novo design, and characterization of an A(2)B(2) diiron protein

21 January 2018

1 reference

12 December 2020

4E binding proteins inhibit the translation factor eIF4E without folded structure

1 reference

12 December 2020

A conformational study of thioredoxin and its tryptic fragments

1 reference

12 December 2020

Sequence and structural analysis of two designed proteins with 88% identity adopting different folds

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1003298

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24204234%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/MitraSBCMGCZ13

29 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_4saxmvmyinaqpaxyevlwgf3ge4

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/4saxmvmyinaqpaxyevlwgf3ge4

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24204234%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

PubMed publication ID

24204234

1 reference