Automated Annotation of Secondary Structure Elements for Entire Protein Families

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Tarakaramji MOTURU, Veronika NAVRÁTILOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Karel BERKA. Automated Annotation of Secondary Structure Elements for Entire Protein Families. In National Bioinformatic Conference ENBIK. 2018.

Basic information

• Original name: Automated Annotation of Secondary Structure Elements for Entire Protein Families
• Authors: MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Tarakaramji MOTURU, Veronika NAVRÁTILOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Karel BERKA.
• Edition: National Bioinformatic Conference ENBIK, 2018.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Faculty of Science

Abstract

Protein structural data, deposited in Protein Data Bank, represent a highly valuable source of information and their amount is continuously growing. Currently, the data contain more and more structurally and functionally similar proteins (so called protein families), which originate from various organisms, contain different ligands, or have various mutations. To analyse and examine these data, we must identify comparable and related regions in different proteins from one protein family. A part of this process is annotation of protein secondary structure elements (SSEs), which form stable parts of the protein and help us to localize the key regions. Since an automated procedure for SSEs annotation is not available yet, we developed such an approach [1]. Our method is template-based, meaning that an annotation of a template protein from the family is provided as an input to the algorithm together with a set of query proteins (the whole family). A three-step algorithm is then executed on each query protein. In the first step, SSEs are detected in the query protein. The second step is structural alignment and superimposition of the query protein and the template protein, so the corresponding parts of the two proteins are located close to each other. The third step is the selection of those SSEs from the query protein which are the best counterparts for the SSEs in the template protein. [1] Svobodová Vařeková, R., Midlik, A., Hutařová Vařeková, I., Hutař, J., Navrátilová, V., Koča, J., Berka, K. (2018). Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. Biophysical Journal, 114(3), 46a-47a.