Refinement of homology-based protein structures by molecular dynamics simulation techniques (Q30886624)

14 November 2017

Refinement of homology-based protein structures by molecular dynamics simulation techniques (English)

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molecular dynamics simulation

14 November 2017

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author name string

Hao Fan

series ordinal

1

1 reference

PMCID

2286528

14 November 2017

Alan E Mark

series ordinal

2

1 reference

14 November 2017

1 January 2004

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14 November 2017

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13

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14 November 2017

1

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14 November 2017

211-220

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PMCID

2286528

describes a project that uses

14 November 2017

molecular dynamics simulation

1 reference

Protein structure prediction in 2002.

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Comparison of performance in successive CASP experiments.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Molecular dynamics in the endgame of protein structure prediction.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Protein structure prediction and structural genomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Prospects for ab initio protein structural genomics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Ab initio protein structure prediction of CASP III targets using ROSETTA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

NMR structure and mutagenesis of the FADD (Mort1) death-effector domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Structures of the reduced and mercury-bound forms of MerP, the periplasmic protein from the bacterial mercury detoxification system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

From Levinthal to pathways to funnels

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Solution structure of the activator contact domain of the RNA polymerase alpha subunit

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

WHAT IF: a molecular modeling and drug design program

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Analysis and assessment of comparative modeling predictions in CASP4.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286528

Do aligned sequences share the same fold?

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/14691236

12 December 2020

inferred from PubMed ID database lookup

Protein modelling for all

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/14691236

12 December 2020

inferred from PubMed ID database lookup

Sequence to structure alignment in comparative modeling using PrISM

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/14691236

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1110/PS.03381404

1 reference

14 November 2017

1 reference

14 November 2017

1 reference

PMCID

2286528