Protein Motif Retrieval by Secondary Structure Element Geometry and Biological Features Saliency

2014 ◽  
Author(s):  
Virginio Cantoni ◽  
Marco Ferretti ◽  
Nicola Pellicano ◽  
Jennifer Vandoni ◽  
Mirto Musci ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Secondary Structure Element ◽  
Protein Motif ◽  
Biological Features

scholarly journals Extension of a de novo TIM barrel with a rationally designed secondary structure element

2021 ◽  
Vol 30 (5) ◽  
pp. 982-989
Author(s):  
Jonas Gregor Wiese ◽  
Sooruban Shanmugaratnam ◽  
Birte Höcker
Keyword(s):  
Secondary Structure ◽  
De Novo ◽  
Secondary Structure Element ◽  
Tim Barrel

Protein Motif Comparator using PSO K-Means

2016 ◽  
Vol 7 (3) ◽  
pp. 56-68 ◽  
Author(s):  
Gowri R. ◽  
Rathipriya R.
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Protein Sequence ◽  
Protein Motif ◽  
Structure Similarity ◽  
Motif Information

The main goal of this paper is to compare the motif information extracted from clusters and biclusters of the protein using Motif Comparator. The clusters and biclusters are obtained using the PSO k-means algorithm. The functions of the proteins are preferably found from their motif information. The Motif Comparator is used to detect the clusters and biclusters, to locate the Significant Amino Acids present, to find the highly homologous cluster. The motif information acquired is based on the structure homogeneity of the protein sequence. The homogeneity is evaluated based on their secondary structure similarity of the protein.

scholarly journals A comparison between internal protein nanoenvironments of α-helices and β-sheets

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244315
Author(s):  
Ivan Mazoni ◽  
Jose Augusto Salim ◽  
Fabio Rogerio de Moraes ◽  
Luiz Borro ◽  
Goran Neshich
Keyword(s):  
Protein Structure ◽  
Secondary Structure ◽  
Univariate Analysis ◽  
Protein Structures ◽  
Main Idea ◽  
Secondary Structure Element ◽  
Statistical Tool ◽  
Full Characterization ◽  
Β Sheets ◽  
Almost All

Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more β-sheets than α helices found inside the protein structures. For example, considering the PDB, DSSP and Stride definitions for secondary structure elements and by using the consensus among those, we found 60,727 helices in 4,376 chains identified in all-α structures and 129,440 helices in 7,898 chains identified in all-α and α + β structures. For β-sheets, we identified 837,345 strands in 184,925 β-sheets located within 50,803 chains of all-β structures and 1,541,961 strands in 355,431 β-sheets located within 86,939 chains in all-β and α + β structures (data extracted on February 1, 2019). In this paper we would first like to address a full characterization of the nanoenvironment found at beta sheet locations and then compare those characteristics with the ones we already published for alpha helical secondary structure elements. For such characterization, we use here, as in our previous work about alpha helical nanoenvironments, set of STING protein structure descriptors. As in the previous work, we assume that we will be able to prove that there is a set of protein structure parameters/attributes/descriptors, which could fully describe the nanoenvironment around beta sheets and that appropriate statistically analysis will point out to significant changes in values for those parameters when compared for loci considered inside and outside defined secondary structure element. Clearly, while the univariate analysis is straightforward and intuitively understood, it is severely limited in coverage: it could be successfully applied at best in up to 25% of studied cases. The indication of the main descriptors for the specific secondary structure element (SSE) by means of the multivariate MANOVA test is the strong statistical tool for complete discrimination among the SSEs, and it revealed itself as the one with the highest coverage. The complete description of the nanoenvironment, by analogy, might be understood in terms of describing a key lock system, where all lock mini cylinders need to combine their elevation (controlled by a matching key) to open the lock. The main idea is as follows: a set of descriptors (cylinders in the key-lock example) must precisely combine their values (elevation) to form and maintain a specific secondary structure element nanoenvironment (a required condition for a key being able to open a lock).

Sign in / Sign up

Export Citation Format

Share Document