This introductory workshop will provide hands-on training on protein and structural bioinformatics resources in the context of molecular dynamics, biomolecular modelling, and simulations. The workshop is sponsored by the Collaborative Computational Project for Biomolecular Simulation (CCPBioSim).
Participants will gain knowledge and skills for searching, selecting, and assessing publicly available protein biodata for use in downstream methods relating to biomolecular modelling and molecular dynamics simulations. The workshop will begin with an introduction to basic concepts in genomics and associated resources, then to protein resources, their uses and limitations, and validation of both experimentally and predicted protein structures.
Finally, the workshop will cover variant effect prediction and offer participants hands-on group projects to bring together the previous days’ training with highly-experienced mentors. During this time, participants will work with simulated datasets to answer small research questions, then present findings thereafter. Participants will also get the chance to network with one another, trainers, and workshop organisers.
Who is this course for?
This workshop is suitable for scientists in any sector performing or using biomolecular modelling, molecular dynamics and/or simulation in their work.
You may be regularly using biodata from various databases but unsure about its quality, how to validate its quality, or know its limitations.
You may have knowledge gaps in biological concepts such as alternative splicing and nuances of genomics, and how this could affect protein sequence, structure and other downstream biological and modelling processes.
You may be new to biomolecular modelling and/or simulation and wish to obtain knowledge and skills around the use of biodata in your work.
Your work can be bioinformatics, computational, wet-lab, or a mix. Experience in basic bioinformatics is not required but may be useful.
Membership of the CCPBioSim community is desirable but not essential to participate. The intended audience for this workshop is broad and you are encouraged to read through the description, learning outcomes and course content to ensure you will benefit. Applications are welcome across the world and please note you do not have to fulfil all the criteria in order to apply for this workshop.
What will I learn?
After the workshop you should be able to:
+ Browse and search EMBL-EBI nucleotide, protein, and structure databases
+ Validate experimentally determined and predicted protein structures
+ Predict the effects of variants on protein structure and function
+ Apply training to small research questions in groups and present findings
Course content
During this workshop, you will learn about:
+ EMBL-EBI nucleotide resources such as: Ensembl, EVA, and ENA
+ EMBL-EBI protein structure resources such as: UniProt, PDBe-KB, and the AlphaFold Database
+ Variant effect prediction tools such as VEP
Applications close: 4 June 2023
Course dates: 19 - 22 September 2023
Course fee: £50.00