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Protein Modelling and Structure-Based Function Prediction

20—21 June 2016

University of Liverpool, UK



Organizers: Daniel J Rigden (University of Liverpool, UK)

                     Luciane V Mello (University of Liverpool, UK)

 

Guest Lecturer: Roman Laskowski (EMBL-EBI, UK)

 

Student Partner: Felix Simkovic (University of Liverpool, UK)

 

 

The two-day event will cover three topics, using interspersed lectures and hands-on sessions. Each day terminates with a one-hour slot in which participants can work on their own data supported by facilitators.

 

1 - Homology Modelling

Concepts and terminology of homology (or comparative) modelling will be introduced and the participants will calculate simple models using the industry-standard tool MODELLER (https://salilab.org/modeller). This will exemplify the additional value of modelling above sequence analysis, as will a Students-as-Partners talk. The results of local, manually-defined modelling and automated servers will then be contrasted and further practical examples used to illustrate the limitations of black-box approaches. 

 

2 - Structure-Based Function Prediction

An overview of structure-based methods for function prediction will be given, focussing on readily available servers and software, especially Profunc (https://www.ebi.ac.uk/thornton-srv/databases/profunc/). Practical examples, of function annotation using a variety of methods will be worked through, including applications for SNP interpretation.


3 - Advanced Modelling Methods

Fragment-based and covariance-based protein modelling will each be introduced in short talks. Participants will then visualise and analyse the different classes of models to understand their value and limitations.


Monday 20 June 2016
09:30 - 10:00 Registration and Refreshments

10:00 - 10:30
Basic Homology Modelling
Lecture
10:30 - 12:00
Basic Homology Modelling
Workshop
12:00 - 12:30
Students-as-Partners Homology Modelling
Presentation
12:30 - 13:30 Lunch

13:30 - 13:45
Advanced Homology Modelling
Lecture
13:45 - 15:00
Advanced Homology Modelling
Workshop
15:00 - 15:15 Refreshment Break

15:15 - 16:00
Structure-Based Function Prediction
Lecture
16:00 - 17:00
Structure-Based Function Prediction
Workshop
17:00 - 18:00
Work with own data
19:45 Conference Dinner

Tuesday 21 June 2016
09:00 - 09:30
Profunc Server
Lecture
09:30 - 11:00
Profunc and SNP
Workshops
11:00 - 11:20 Refreshment Break

11:20 - 12:30
Protein Modelling
Competition
12:30 - 13:00
Results of Competition
Discussion
13:00 - 14:00 Lunch

14:00 - 14:30
Fragment-Based Modelling
Lecture
14:30 - 15:00
Fragment-Based Modelling
Workshop
15:00 - 15:15 Refreshment Break

15:15 - 15:45
Covariance-Based Modelling
Lecture
15:45 - 16:15
Covariance-Based Modelling
Workshop
16:15 - 17:00
Work with own data