Dear Sameer and Joana, I am a postdoctoral researcher in Helen Ginn’s Protein Machinists group at DESY, with a background in applied mathematics and a PhD in protein crystallography from the University of Surrey. My work spans experimental data analysis, model building, and software development for structural biology.
I am very interested in the ARISE2 fellowship opportunity you are mentioning and would like to check whether an idea I have in mind would be a good match for your project’s scope before preparing a formal proposal. My concept builds on prior efforts to curate crystallisation data to fill a critical gap: the absence of systematically reported negative outcomes. I propose developing a large-scale, well-structured, open-access database that brings together both successful and unsuccessful crystallisation trials. By collaborating with the Bowman Lab and the US National Crystallisation Center, who have made in the recent years some notable progress in curating such data, we can integrate these resources with sequence and structural annotations. As part of the project, I would also explore a collaboration with EMBL Hamburg’s Sample Preparation and Characterisation (SPC) facility to incorporate additional experimental context from their high-throughput crystallisation platform. The final goal is to use the resulting dataset to support AI model for predicting crystallisation conditions for novel proteins and variants, with the aim of providing a useful, FAIR-compliant resource for the wider community. Do you think this approach could align well with your focus on creating training datasets and developing AI methods for structural biology within ARISE2? Thank you very much for your time and consideration. Best regards, Virginia Apostolopoulou Postdoctoral Researcher, Protein Machinists, DESY [email protected] > On 4 Aug 2025, at 10:46, Sameer Velankar <[email protected]> wrote: > > Dear CCP4 Community, > We are excited to announce a unique postdoctoral opportunity for a STEM > professional to work on innovative AI applications in structural biology > through the ARISE2 MSCA-funded fellowship programme. > > Our project, led by the Pereira <https://pereiralab.sites.vib.be/en> and > Velankar <https://www.ebi.ac.uk/people/person/sameer-velankar/> teams, aims > to tackle computational challenges in predicting protein function using > AI-based approaches. Our work will focus on: > Using structural and sequence data to create training and benchmark datasets > for developing AI methods > Developing advanced AI techniques to predict protein function > Utilising Knowledge Graph (KG) techniques to provide enriched functional > annotations, facilitating more effective data interpretation and knowledge > transfer between related proteins. > > Location and Duration > Primary Location: EMBL-EBI, Cambridge, UK > Regular collaboration and visits to VIB AI in Leuven, Belgium, are expected. > The position is for 3 years. > > Application > Please submit a two-page CV and a two-page project proposal related to the > area outlined above to Sameer Velankar at [email protected] > <mailto:[email protected]> and [email protected] > <mailto:[email protected]> by 5 September 2025. > > The two-page proposal should cover the following areas - > Background, proposed project > Expected results & their impact > Service to be offered > Consideration of FAIR principles > > This is a preliminary proposal. In the second step, we will select one > candidate by 16 September at the latest. The selected candidate will then > submit a full proposal by the deadline for the ARISE2 call on 30 September. > > More information about the ARISE2 programme can be found at > https://www.embl.org/training/arise2/ > Please take a look at the guidelines and project proposal template available > on the ARISE2 website > <https://www.embl.org/training/arise2/#vf-tabs__section-apply>. > > Contacts: > For this application > Sameer Velankar <[email protected] <mailto:[email protected]> > Joana Pereira <[email protected] <mailto:[email protected]>> > For questions about the ARISE2 programme > [email protected] <mailto:[email protected]> > > > Best Wishes, > Sameer and Joana > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
