Lecture and Exercise Protein Prediction I for Bioinformaticians SS16

Topics will include (but not be limited to):

• Intro: what is protein function?
• Predicting protein function using sequence: sequence alignments, multiple sequence alignments, motifs, domain assignment, annotation transfer by homology, ab initio predictions.
• Predicting protein function using structure: structural alignments, structural motifs, annotation transfer via structure similarity.
• From structure prediction to function prediction: comparative modeling; prediction of: secondary structure, hydrophilicity profiles, solvent accessibility, transmembrane segments, disordered regions, contact maps, functional residues; template free modeling.
• Machine learning.

Slides:

• Apr 19th Intro
• Apr. 21st Intro2 – video
• Apr. 26th 3D comparison – video
• Apr. 28th Sequence Alignments – video
• May 3rd Alignments – video
• May 12th Comparative Modeling Experimental Structure Determination – video
• May 24th Mechanisms
• May 31st Secondary Structure – video
• Jun 2nd Transmembrane Helices – video
• Jun 7th Transmembrane Helices 2 – video
• Jun 9th TMSEG – video Note: TMSEG predicts ~4 protein per second, not per minute. That's pretty fast :)
• Jun 14th Membrane Structure Prediction – video
• Jun 16th Intrinsically Disordered Proteins – video

Exercise:

• The exercise is managed exclusively through this wiki page that will be maintained throughout the course.
• Please find all materials and announcements here
• This page requires log-in information which can be obtained from the tutors during the exercise sessions