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.