Multiple Sequence Alignment with Jalview and Protein Structure and Function

Date: Monday 14th to Tuesday 15th May 2018
Time: 9.00 to 17.00
Location: MSTC, Sherrington Building, University of Liverpool, L69 3BX

Overview
This two day hands-on training course is aimed at students and researchers who want to gain practical understanding of the tools and approaches for protein sequence, structure and function prediction and analysis.

In day 1, participants will be introduced to Jalview - a free desktop application for the visualisation and comparative analysis of protein, DNA and RNA sequences. Jalview can integrate data from Ensembl, Uniprot, PDBe, Rfam and Pfam, and can access a range of tools for multiple sequence alignment, conservation analysis and secondary structure and disorder prediction, including the widely used JPred4.

On the second day, participants will learn to use Jalview’s 3D structure visualisation capabilities in conjunction with UCSF Chimera, and take a whistle-stop tour of the methodologies and tools for prediction and analysis of Protein 3D structure and function. Participants are encouraged to bring their own protein analysis problems and time will be reserved at the end of day 2 for discussion.

Please use this link to register:  https://goo.gl/forms/wfq4oA2tficLErqV2

Day 1: Multiple Sequence Alignment and Analysis with Jalview
Workshop trainers: Dr Jim Procter and Dr Suzanne Duce

9    9.15    Introduction to the Workshop
9.15    10.30    Session 1.Loading sequences, structures and alignments with Jalview
Coffee break
11    12.30    Session 2. Multiple alignment Creation and Alignment Reliability
Lunch
1.30    3pm    Session 3. Phylogenetic trees and subfamily analysis of Proteins and CDS
Coffee break
3.30    5pm    Session 4. Protein secondary structure and disorder prediction, and working with annotation

Day 2: Protein Structure Analysis and Modelling
Workshop trainers: Dr Jim Procter and Dr Dan Rigden

9    9.15    Introduction to Workshop Day 2
9.15    9.30    Introduction to Protein 3D Structure
9.30    10    Viewing and Comparing 3D structures with Jalview and UCSF Chimera
10    10.30    Mapping sequence conservation to Biological Assemblies with Jalview
Coffee Break
11    12.30    Functional analysis of Protein Structures
Lunch
1.30    2.30    Homology modelling and model quality evaluation
2.30    3.15    Ab initio models and searching for fold matches
3.15    3.30    Wrap up: Function Analysis and 3D models
Coffee Break
4pm    5pm    Analyse your own protein sequences and structures.

Start Date: 
14-05-2018 to 15-05-2018
location: 
Sherrington Building, University of Liverpool, L69 3BX
Duration: 
2 days