Protein Prediction I for Computer Scientists

Module IN2322

This Module is offered by TUM Department of Informatics.

This module handbook serves to describe contents, learning outcome, methods and examination type as well as linking to current dates for courses and module examination in the respective sections.

Basic Information

IN2322 is a semester module in English language at Master’s level which is offered in summer semester.

This Module is included in the following catalogues within the study programs in physics.

  • Catalogue of non-physics elective courses
Total workloadContact hoursCredits (ECTS)
240 h 90 h 8 CP

Content, Learning Outcome and Preconditions

Content

Intro: What is a protein? What is protein structure & function? Prediction of protein structure: overview. 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 into machine learning with particular focus on how to avoid over-estimating performance.

Learning Outcome

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.

Preconditions

none

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

ArtSWSTitelDozent(en)Termine
VU 6 Protein Prediction I Beginners (IN2322) Dienstag, 09:00–11:30
Donnerstag, 10:00–12:30
Donnerstag, 12:30–14:00
Donnerstag, 12:30–14:00

Learning and Teaching Methods

Lectures, Exercises, Questions & Answers sessions

Media

Lectures presented in form of interactive seminars using projector and white board; some lectures will be given on the white board, only. All lectures will be video taped and both the slides and the recordings will be made available shortly after the lecture.

Literature

Will be announced in the lecture.

Module Exam

Description of exams and course work

The module is graded by a written exam. The exam will take 80 - 120 minutes. In the exam the participants demonstrate their ability to devise and discuss an appropriate computational approach for a solution for 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 they can choose the appropriate data abstraction level (1D, 2D, 3D) depending to 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 pro's and con's 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. Details are announced at the beginning of the lecture

Exam Repetition

There is a possibility to take the exam at the end of the semester.

Current exam dates

Currently TUMonline lists the following exam dates. In addition to the general information above please refer to the current information given during the course.

Title
TimeLocationInfoRegistration
Protein Prediction I for Computer Scientists
Di, 18.10.2016, 18:00 bis 19:30 MW: 0001
registration period extended till 30th Sept bis 30.9.2016 (Abmeldung bis 11.10.2016)

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When atoms interact things can get interesting. Fundamental research on the underlying properties of materials and nanostructures and exploration of the potential they provide for applications.

Nuclei, Particles, Astrophysics

A journey of discovery to understanding our world at the subatomic scale, from the nuclei inside atoms down to the most elementary building blocks of matter. Are you ready for the adventure?

Biophysics

Biological systems, from proteins to living cells and organisms, obey physical principles. Our research groups in biophysics shape one of Germany's largest scientific clusters in this area.