Pro-/Seminar: Bioinformatics of Protein-Protein Interactions

Lecturer:

Prof. Dr. Volkhard Helms

Tutor

Nicolas Künzel, Email: nicolas.kuenzel[at]bioinformatik.uni-saarland.de

Maximum number of participants:

12

Lecture:

block seminar: Wednesday – Friday, October 10th – 12th, 1:00 pm – 6:00 pm, E2 1. room 007

 

Preliminary meeting and placement of the topics:

Wednesday, July 18th, 2018, 3:00 pm, E2 1, room 007

Requirements:

Knowledge corresponding to semester 4 (proseminar) or knowledge corresponding to BSc degree (seminar)

Conditions for certification:

Successful presentation, regular participation (at least 60% of talks)

Leistungspunkte/Credits:

5 (proseminar) or 7 (seminar)

Additional Information:

Please regard the important hints for your seminar presentation!

Timetable for the talks:

Wednesday, Oct. 10 Thursday, Oct. 11 Friday, Oct. 12
 1  5  10
 2  6  11
 3  7  12
 4  9

 

Topics:

  1. Statistics of protein-protein contacts
  2. Integrative structure determination of protein-protein complexes
  3. Protein-protein docking: algorithms + scoring methods + results (ClusPro)
  4. Co-evolutionary restraints + application in protein-protein docking (Gremlin) Only as seminar topic
  5. Binding free energy models for protein-protein complexes (Vangone & Bonvin) Only as proseminar topic
  6. Predicting hot spot residues at protein interfaces + machine learning
  7. Principles of Molecular dynamics simulations + MD simulations of protein-protein complexes Paper 1 Paper 2
  8. Principles of Brownian dynamics simulations + BD simulations of protein protein encounter
  9. Markov state models for protein ligand association Only as seminar topic
  10. Mutation-induced changes of PP binding affinity
  11. Effects of alternative splicing on protein complexes
  12. Phosphorylation-mediated protein interaction switches