Syllabus for Structural Bioinformatics

Learning outcomes

After completing the course, the student should be able to

• explain the relationship between protein sequence and protein structure
• describe how structure translates into function within different biological fields such as catalysis, transport and regulation
• estimate the validity of information in macromolecular structure databases, and use computer programs to visualise and analyse macromolecular structures from a functional perspective
• use bioinformatics tools for sequence alignment, sequence motif identification and prediction of secondary and tertiary structures
• account for the purpose, theoretical background, ethical aspects and limitations of the above mentioned bioinformatics methods and use this knowledge to interpret relevant results.

Content

Relation between sequence, structure and function. Structural basis for macromolecular dynamics, binding specificity and catalysis.

Overview of biological databases, servers and information centres. Sequence comparisons. Basic macromolecular structure: three-dimensional structure, PDB co-ordinates, classification of proteins in structure families, programs for analysis and comparison of structures. Introduction to the theory of classification and comparison of sequences and extraction of common distinctive features (e.g., motifs). Sequence analysis for prediction of secondary and tertiary structures, and homology modelling of three-dimensional structures based on sequence data. Research and publication ethics.

Instruction

Lectures, seminars and computer exercises. Attendance at seminars and full participation in computer labs is mandatory to pass the course.

Assessment

Written examination ( 3 credits) , laboratory, exercises and seminars ( 2 credits) .