Structure‐based classification of FAD binding sites: A comparative study of structural alignment tools

@article{Garma2016StructurebasedCO,
  title={Structure‐based classification of FAD binding sites: A comparative study of structural alignment tools},
  author={Leonardo D. Garma and Milagros Medina and Andr{\'e} H. Juffer},
  journal={Proteins: Structure},
  year={2016},
  volume={84}
}
A total of six different structural alignment tools (TM‐Align, TriangleMatch, CLICK, ProBis, SiteEngine and GA‐SI) were assessed for their ability to perform two particular tasks: (i) discriminating FAD (flavin adenine dinucleotide) from non‐FAD binding sites, and (ii) performing an all‐to‐all comparison on a set of 883 FAD binding sites for the purpose of classifying them. For the first task, the consistency of each alignment method was evaluated, showing that every method is able to… 

Structural bioinformatics tools for the comparison and classification of protein interactions

The results indicate that both the known protein-protein and the protein-FAD interactions can be classified into a reduced number of types and that in general terms these classifications are consistent with the proteins' functions.

Binding Site Comparison - Software and Applications

AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models

AppA is developed, a web server that can be used to analyze and compare 3D structures of contact residues and interfacial waters of antibody–antigen complexes and is the first web server equipped with the capability for dissecting the contributions of interfacial water molecules, hydrogen bonds, hydrophobic interactions, van der Waals interactions and ionic interactions at the antibody-antigen interface.

On the origin of vanillyl alcohol oxidases.

References

SHOWING 1-10 OF 51 REFERENCES

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

A new COFACTOR webserver for automated structure-based protein function annotation and was ranked as the best method for protein–ligand binding site predictions in the recent community-wide CASP9 experiment.

CLICK—topology-independent comparison of biomolecular 3D structures

The server, CLICK, is capable of superimposing the 3D structures of any pair of biomolecules with the option of using other structural features such as secondary structure, solvent accessible surface area and residue depth to guide the alignment.

Sequence‐structure analysis of FAD‐containing proteins

No single protein ‘pharmacophore’ exists for binding FAD, and in every FAD‐binding family, the pyrophosphate moiety binds to the most strongly conserved sequence motif, suggesting that pyroph phosphate binding is a significant component of molecular recognition.

Scoring function for automated assessment of protein structure template quality

A new scoring function, the template modeling score (TM‐score), to assess the quality of protein structure templates and predicted full‐length models by extending the approaches used in Global Distance Test (GDT) 1 and MaxSub, which suggests that the TM‐score is a useful complement to the fully automated assessment ofprotein structure predictions.

Pocket Similarity: Are α Carbons Enough?

A novel method for measuring protein pocket similarity was devised, using only the alpha carbon positions of the pocket residues, which found that a specificity of 99.2% and sensitivity of 97.5% could be achieved using an appropriate cutoff score.

Efficient Identification of Critical Residues Based Only on Protein Structure by Network Analysis

A new algorithm based on network analysis applied exclusively on protein structures to identify critical residues with high reliability is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures.

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

There exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB, which could be used to assist in model selection in blind protein structure predictions.

Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non‐enzyme families

This study aims to investigate the performance of residue centrality, viewed as a family fold characteristic, in identifying functionally important residues in protein families, and focuses on binding sites, to identify key residues for the integration and transmission of the information to the rest of the protein, reflecting the relationship between fold and function.
...