- EMBO-hosted webpage for the course
- Twitter search results for #EMBOPPI2018
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 09:00 - 09:15 | Course Begins | Allegra Via | Introduction to the Course and Speakers |
| 09:15 - 10:00 | Overview lecture | Toby Gibson | Computational analysis of protein-protein interactions in cell function |
| 10:00 - 10:30 | Icebreaker & coffee break | - | - |
| 10:30 - 11:30 | Lecture & Demo | Marco Punta | Resources for Protein families, protein domains and protein complexes - I |
| 11:30 - 13:00 | Practical | Marco Punta | Resources for Protein families, protein domains and protein complexes - II |
| 13:00 - 14:15 | Lunch break | - | - |
| 14:15 - 15:00 | Practical | Marco Punta | Resources for Protein families, protein domains and protein complexes - II (continued) |
| 15:00 - 16:00 | Lecture & Practical | Natasha Wood | Web resources describing results of PPI experiments; design of such databases, minimal information to describe PPIs |
| 16:00 - 16:30 | Icebreaker & coffee break | - | - |
| 16:30 - 17:30 | Lecture & Practical | Lars Juhl Jensen | Protein association networks with STRING: Lecture & Practical |
| 17:30 - 18:30 | Lecture & Demo | Scooter Morris | Introducing network analysis using Cytoscape |
| 19:30 onwards | Dinner | - | - |
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 09:00 - 10:00 | Plenary Talk | Natasha Wood | Understanding PPI and drug-resistance profiles of HIV-1 protein variants using molecular dynamics |
| 10:00 - 10:30 | Coffee break | - | - |
| 10:30 - 12:00 | Lecture & Demo | Scooter Morris & Lars Juhl Jensen | Gaining insights into networks using Cytoscape |
| 12:00 - 13:00 | Practical | Scooter Morris, Nadezhda Doncheva & Lars Juhl Jensen | Analysis and visualization of PPI networks using Cytoscape and stringApp |
| 13:00 - 14:00 | Lunch break | - | - |
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 14:00 - 15:30 | Practical | Toby Gibson | Revealing interactive features in protein multiple sequence alignments with Jalview |
| 15:30 - 16:00 | Coffee break | - | - |
| 16:00 - 18:00 | Public Unseminar | Malvika Sharan and Holger Dinkel | Bioinformatics Tool-omics - optional informal discussion and activity |
| 19:30 onwards | Dinner | - | - |
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 09:00 - 09:30 | Lecture | Scooter Morris | Protein structure databases and Chimera tool to explore structure |
| 09:30 - 10:30 | Practical & Demo | Scooter Morris | Visualizing protein structures and interaction interfaces with UCSF Chimera |
| 10:30 - 11:00 | Coffee break | - | - |
| 11:00 - 12:30 | Practical | Scooter Morris | Visualizing very large protein complexes with UCSF ChimeraX |
| 12:30 - 14:30 | Poster session | - | - |
| 14:30 onward | Excursion and dinner | - | - |
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 09:00 - 10:30 | Lecture & Practical | Zsuzsanna Dosztányi | Biology and prediction of intrinsically unstructured peptide regions [Exercises] |
| 10:30 - 11:00 | Coffee break | - | - |
| 11:00 - 11:30 | Lecture | Holger Dinkel | Introduction of Linear motifs and IDRs |
| 11:30 - 13:00 | Practical | Holger Dinkel & Toby Gibson | Linear motif biology and prediction, cooperativity in cellular signaling (I) |
| 13:00 - 14:00 | Lunch break | - | - |
| 14:00 - 15:00 | Practical | Holger Dinkel & Toby Gibson | Linear motif biology and prediction, cooperativity in cellular signaling (II) |
| 15:00 - 16:30 | Lecture & Practical | Miguel Andrade | Structure and interactions of repeated and low complexity IDRs in proteins (MR1.fasta) |
| 16:30 - 17:00 | Coffee break | - | - |
| 17:00 - 18:30 | Option-1: Practical session | Hands-on session on the presented tools with the trainers | Work on own/publicly available disease data |
| 17:00 - 18:30 | Option-2: Practical session | Holger Dinkel | Linear motif biology and prediction, cooperativity in cellular signaling III: automated access of online tools using REST interfaces [Exercises] |
| 19:30 onwards | Dinner | - | - |
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 09:00 - 10:00 | Plenary Talk | Norman Davey | Discovery of transient protein-protein interactions |
| 10:00 - 10:30 | Coffee break | - | - |
| 10:30 - 11:30 | Practical | Scooter Morris | Visualising complexes connected with XL-MS data using UCSF Chimera |
| 11:30 - 12:10 | Lecture | Allegra Via | PPI 3D complex prediction and interfaces (What we talk about when we talk about docking) |
| 12:10 - 12:30 | Lecture | Lars Juhl Jensen | Disease network mining |
| 12:30 - 14:00 | Practical | Scooter Morris, Nadezhda Doncheva & Lars Juhl Jensen | Network clustering and enrichment analyses in Cytoscape |
| 14:00 - 15:00 | Lunch break | - | - |
| 15:00 - 16:00 | Practical | Scooter Morris & Nadezhda Doncheva | Using Cytoscape to integrate protein complex data (CORUM, Complexes portal) into PPI networks |
| 16:00 - 16:30 | Coffee break | - | - |
| 16:30 - 17:30 | Plenary talk | Gianni Cesareni | Investigating the protein interaction network supporting the skeletal muscle regeneration program |
| 17:30 - 19:00 | Practical session | Hands-on session on the presented tools with the trainers | Work on own/publicly available disease data |
| 19:30 onwards | Dinner | - | - |
| Time | Activity | Responsible | Title |
|---|---|---|---|
| 09:00 - 10:00 | Practical session | Miguel Andrade | Exploring tools for modules that promote protein aggregation [Random UniprotId] |
| 10:00 - 10:30 | Coffee break | - | - |
| 10:30 - 12:00 | Practical session | Hands-on session on the presented tools with the trainers | work on own/publicly available disease data |
| 12:00 - 12:45 | Summary | Group Presentation | Putting everything in perspective: Shared files for the group task |
| 12:45 - 13:00 | Final Q&A session and wrap-up | - | - |
| Time will be announced | Dinner | - | - |