Sampling bottlenecks in de novo protein structure prediction (Q30379441)

3 November 2017

Sampling bottlenecks in de novo protein structure prediction (English)

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protein structure prediction

3 November 2017

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David Baker

4

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author name string

David E Kim

series ordinal

1

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3 November 2017

Ben Blum

series ordinal

2

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3 November 2017

Philip Bradley

series ordinal

3

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3 November 2017

language of work or name

English

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publication date

28 July 2009

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Journal of Molecular Biology

3 November 2017

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3 November 2017

393

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3 November 2017

1

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3 November 2017

249-260

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describes a project that uses

3 November 2017

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/2760740

based on heuristic

inferred from PubMed Central ID database lookup

cites work

De novo protein structure generation from incomplete chemical shift assignments.

1 reference

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Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

20 June 2018

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Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.

20 June 2018

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Crystal and molecular structure of chymotrypsin inhibitor 2 from barley seeds in complex with subtilisin Novo

20 June 2018

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Physically realistic homology models built with ROSETTA can be more accurate than their templates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

Progress in modeling of protein structures and interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

Free modeling with Rosetta in CASP6

20 June 2018

1 reference

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Toward high-resolution de novo structure prediction for small proteins.

20 June 2018

1 reference

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Progress and challenges in high-resolution refinement of protein structure models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

Protein structure prediction using Rosetta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

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

20 June 2018

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Cyclic coordinate descent: A robotics algorithm for protein loop closure.

20 June 2018

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Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation

20 June 2018

1 reference

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Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome

20 June 2018

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Protein secondary structure prediction based on position-specific scoring matrices

20 June 2018

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The yhhP gene encoding a small ubiquitous protein is fundamental for normal cell growth of Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

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

20 June 2018

1 reference

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Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

The folding pathway of a protein at high resolution from microseconds to seconds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

Automatic classification and analysis of alpha alpha-turn 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=2760740

Identification, classification, and analysis of beta-bulges 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=2760740

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=2760740

Ubiquitin folds through a highly polarized transition state.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760740

Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19646450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19646450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JMB.2009.07.063

1 reference

3 November 2017

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3 November 2017

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