Structural classification of thioredoxin‐like fold proteins

@article{Qi2005StructuralCO,
  title={Structural classification of thioredoxin‐like fold proteins},
  author={Yuan Qi and Nick V. Grishin},
  journal={Proteins: Structure},
  year={2005},
  volume={58}
}
Protein structure classification is necessary to comprehend the rapidly growing structural data for better understanding of protein evolution and sequence–structure–function relationships. Thioredoxins are important proteins that ubiquitously regulate cellular redox status and various other crucial functions. We define the thioredoxin‐like fold using the structure consensus of thioredoxin homologs and consider all circular permutations of the fold. The search for thioredoxin‐like fold proteins… 

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References

SHOWING 1-10 OF 66 REFERENCES

SCOP: a structural classification of proteins database

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures that provide the basis of the ASTRAL sequence libraries that can be used as a source of data to calibrate sequence search algorithms and for the generation of statistics on, or selections of, protein structures.

Identification of homology in protein structure classification

The discrimination between analogy and homology of close structural neighbors will lead to functional predictions while avoiding overprediction, allowing fast, self-consistent and complete classification of large numbers of protein structures.

Identification and classification of protein fold families.

Analysis of sequence and structure conservation within the larger families shows the globins to be the most highly conserved family and the TIM barrels the most weakly conserved.

KH domain: one motif, two folds.

Analysis of spatial structures of KH domains in hnRNP K and S3 reveals that they are topologically dissimilar and thus belong to different protein folds, providing a rare example of protein domains that share significant sequence similarity in the motif regions but possess globally distinct structures.

Dictionary of recurrent domains in protein structures

A method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and recurrence is presented, which yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone.

The CATH protein family database: A resource for structural and functional annotation of genomes

Recent developments to the CATH domain database of protein structural families are described which have facilitated genome annotation and which have also revealed important caveats that must be considered when transferring functional data between homologous proteins.

Random circular permutation of DsbA reveals segments that are essential for protein folding and stability.

It is suggested that random circular permutation allows identification of contiguous structural elements in a protein that are essential for folding and stability.
...