Protein Structure Similarity Clustering: Dynamic Treatment of PDB Structures Facilitates Clustering

Protein structure similarity clustering: dynamic treatment of PDB structures facilitates clustering.

Data Clustering and Similarity

In this article, we study the notion of similarity within the context of cluster analysis. We begin by studying different distances commonly used for this task and highlight certain important properties that they might have, such as the use of data distribution or reduced sensitivity to the curse of dimensionality. Then we study interand intra-cluster similarities. We identify how the choices m...

BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum

The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, exper...

Conserved residue clustering and protein structure prediction.

Protein residues that are critical for structure and function are expected to be conserved throughout evolution. Here, we investigate the extent to which these conserved residues are clustered in three-dimensional protein structures. In 92% of the proteins in a data set of 79 proteins, the most conserved positions in multiple sequence alignments are significantly more clustered than randomly se...

Protein cavity clustering based on community structure of pocket similarity network

Functions of a protein are mainly determined by its structure. Surface cavities, also called pockets or clefts, are ordinarily regarded as potentially active sites where the protein carries out the functions. Clustering these pockets is a challenging task in structural genomics. In this paper, we introduce pocket similarity network which possesses the feature of community structure to systemati...