Protein Prediction I for Computer Scientists

Introduction: What is a protein? What is protein structure & function? Overview of methods predicting protein structure.
Methods: Sequence comparisons (sequence-sequence, sequence-profile, profile-profile, HMM); prediction of protein structure in 1D (secondary structure, solvent accessibility, membrane helices), 2D (contact prediction methods, contemporary methods using correlated mutations), 3D (comparative modeling, MD); prediction of disorder in proteins.
The lectures include an introduction to machine learning with particular focus on how to avoid over-estimating performance.

Students understand the basic principles in protein sequence analysis, in protein structure and protein structure prediction. They understand the biological and computer science background of the methods toward these objectives in computational biology.
Students have acquired the theoretical background consisting of the presented knowledge to develop and implement simple independent solutions towards the presented problems.

None

Lectures, Exercises, Questions & Answers (Q&A) sessions
Lectures (include Q&A): Theoretical background for all topics will be presented in traditional lecture style with slides, as well as, interactively through white board presentations and Q&A sessions.
Exercises (include Q&A): Practical programming exercises deepening and applying the material presented in the lectures; occasionally, presentation of additional material needed for better understanding; exercises also include interactive Q&A sessions, and presentations from the students.

Lectures presented as interactive seminars using projector and white board; some lectures will be given on the white board, only. If supported: All lectures will be video-taped and both the slides and the recordings will be made available shortly after the lecture.

Will be announced in the lecture. For formal reasons: Anna Tramontano: Introduction to Bioinformatics, or Arthur Lesk: Introduction to Bioinformatics, or Amit Kessel & Nir Ben-Tal: Introduction to Proteins

The module is graded by a written exam at the end of the semester. The exam takes 120 minutes.
Weekly programming exercises and questions are graded and contribute to 50% of the final grade.
In the exam the participants demonstrate their ability to devise and discuss an appropriate computational approach for a solution to a biological problem in the area of structure prediction. For example, they choose the appropriate methods depending on the type of data they have (1D, 2D, 3D) as well as the appropriate data abstraction level (1D, 2D, 3D) depending on the respective biological question. They demonstrate their understanding of the concepts in the choice of appropriate solution approaches to the given tasks and they can evaluate these in terms of a discussion of the various pros and cons of alternative approaches in biological as well as in technical aspects. They can demonstrate their ability to create a usable tool implementing a solution approach down to the level of pseudo-code. More details are announced at the lecture beginning.