Protein structural bionformatics

Course unit

title

Scientific direction

Scientific code

Faculty

Department (s)

Protein structural bionformatics

Biochemistry N 004

Biology N 010

Informatics N 009

Life Sciences Center

Institute of Biotechnology

Mode of studies

Number of credits

Mode of studies

Number of credits

Lectures

0

Consultations

0

Self-studies

8

Seminars

0

Aims of course

To improve understanding and to acquire new knowledge of application of computational methods for the analysis of protein sequence, structure and function as well as for computational prediction of protein structure and function.

Main topics

Major databases of protein sequence and structure data; PDB as the central database of experimentally determined structures of biological macromolecules; the concept of amino acid similarity; protein homology; detection of protein similarity; representation of generalized information about protein family using sequence profiles an hidden Markov models; protein secondary and tertiary structure; the relationship between protein sequence, structure and function and the use of computational methods for studying this relationship; protein-protein interactions and protein assemblies; computational prediction of 3D structure of proteins and protein assemblies; estimation of accuracy of protein structural models.

Main literature

• Structural bioinformatics/edited by Jenny Gu, Philip E. Bourne. (2nd ed., p. xxvi). (2009). Hoboken [N.J.] : Wiley-Blackwell, c2009.
• A.Lesk. Introduction to Bioinformatics, 4th editition // Oxford University Press, 2014, ISBN-13 978-0199651566.
• Understanding bioinformatics / Marketa Zvelebil & Jeremy O. Baum (2007) Garland Science, ISBN 9780815340249.
• Homology modeling : methods and protocols / edited by Andrew J.W. Orry, Ruben Abagyan. Volume 857, 2012 // Humana Press, ISBN: 978-1-61779-587-9 (Print) 978-1-61779-588-6 (Online).
• State-of-the-art web services for de novo protein structure prediction, Briefings in Bioinformatics, 2020; https://doi.org/10.1093/bib/bbaa139
• Original and review articles describing new computational methods (a regularly updated list).

Assessment strategy

Assessment criteria

Assessment is based on the completion of the assigned practical task. The methods used and the results obtained should be provided in a written form befor the exam and presented to the commission during the exam.

The timeframe allocated for the completion of the assigned practical task is flexible (up to several months). The assessment is based on a written report and on the oral presentation during the exam. The assessment includes several major points. Are the applied methods adequate and sufficient to complete the task? Can the doctoral student make the case for selecting this or that method to complete the task? Does the doctoral student has at least a general understanding of how the selected methods work? Are the derived conclusions coherent with the results obtained?

Česlovas Venclovas

Approved by the Council of Doctoral School of Life Sciences Center No (4.10)600000-KT-… on the 14th of October 2021

Chairman dr. Daiva Baltriukienė