OverProt: secondary structure consensus for protein families

Abstract

Summary Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and β-connectivity. Availability and implementation OverProt Server is freely available at https://overprot.ncbr.muni.cz. Supplementary information Supplementary data are available at Bioinformatics online.

SSDraw: Software for generating comparative protein secondary structure diagrams

“…Multiple diagrams from one MSA can be generated and stacked for easy comparison. These functionalities distinguish SSDraw images from other secondary structure visualizations (Gouet et al, 2003 ; Hutarova Varekova et al, 2021 ; Hutchinson & Thornton, 1990 ; Kocincova et al, 2017 ; Midlik et al, 2022 ; O'Donoghue et al, 2015 ; Stivala et al, 2011 ). For instance, ESPript (Gouet et al, 2003 ) relates secondary structures derived from one representative protein structure to multiple homologous sequences, usually divided on multiple lines of text.…”

SSDraw: software for generating comparative protein secondary structure diagrams

“…Multiple diagrams from one MSA can be generated and stacked for easy comparison. These functionalities distinguish SSDraw images from other secondary structure visualizations [22][23][24][25][26][27][28] . For instance, ESPript 23 relates secondary structures derived from one representative protein structure to multiple homologous sequences, usually divided on multiple lines of text.…”