skip to content
Dovepress - Open Access to Scientific and Medical Research
View our mobile site

8838

Assessing 3D scores for protein structure fragment mining

Original Research

(1779) Views  (408) Full article downloads

Authors: Frédéric Guyon, Pierre Tufféry

Published Date July 2010 Volume 2010:2 Pages 67 - 77
DOI: http://dx.doi.org/10.2147/OAB.S6960

Frédéric Guyon1, Pierre Tufféry1,2

1MTi, INSERM UMR-S973, Université Paris Diderot-Paris 7, Paris, France; 2RPBS, Université Paris
Diderot-Paris 7, Paris, France

Abstract: Quantifying the 3D similarity between two proteins is a difficult task that has motivated the assessment of several 3D scores. New developments in protein modeling and analysis have led to the emergence of new interest towards mining structures at the local level. We assess in the context of fragment mining several dissimilarity scores. We revisit the concept of mirror conformation previously introduced at the level of complete structures and extend it to the more local level. We also consider an explicit criterion measuring the fragment boundary discrepancies. Whereas classical criteria such as the root mean square deviation (RMSd) fail to identify similar shapes in a consistent way, we show that local mirror and boundary mismatch filtering greatly supplements classical scores to select significant matches. The geometrical conditions defined by such criteria can be considered as signatures of fragment similarity. Furthermore, it is possible to tune the degree of similarity depending on the size of the mirrors accepted. This results in a more intuitive perception of the concept of similarity, and opens new perspectives for the rapid mining of large collections of structures.

Keywords: protein fragments, similarity, distance, mining









Readers of this article also read:

Role of aliskiren in cardio-renal protection and use in hypertensives with multiple risk factors
Balancing false discovery and false negative rates in selection of differentially expressed genes in microarrays
Refinement of rigid-body protein–protein docking using backbone and side-chain minimization with a coarse-grained model
Computational methods for the identification of microRNA targets
Efficiency of a hierarchical protocol for high throughput structure-based virtual screening on GRID5000 cluster grid
Molecular docking studies on the activity of naturally occurring pyranochalcones on the transcriptional regulator enzyme of Pseudomonas putida
Ligand competition assays indicate allosterism and insufficiency of the ternary complex model
The interpretation of protein structures based on graph theory and contact map
Antioxidant oils and Salmonella enterica Typhimurium reduce tumor in an experimental model of hepatic metastasis
Cumulative clinical experience from over a decade of use of levofloxacin in community-acquired pneumonia: critical appraisal and role in therapy