Jordan Dialpuri

Automated model building of protein-nucleotide complexes using X-ray data and Alphafold models

About me

I graduated from the University of York with a First with Distinction in Chemistry (MChem) in 2022. During my undergraduate degree I was always very interested in computational chemistry and programming. After my third year, I completed a summer project with Dr Jon Agirre which allowed me to extend my knowledge of computational science. This experience dramatically increased my competency in Python, however, it was the realisation that my work would help a wide variety of scientists from across the world that really motivated me. This work gave me real experience as to how computational research is completed and reaffirmed my interest in continuing my studies with a PhD. Fortunately, Dr Jon Agirre and Professor Kevin Cowtan had a PhD studentship available which aligned with my interests of creating software tools to help scientists. 

My Project

X-ray crystallography is one of the main tools used to elucidate the structure of macromolecules. After the experiment, there are a large number of steps required to obtain an accurate and representative model. One of the most important steps is actually building an atomic model into an electron density map. This step can be done manually but is laborious for large protein or nucleic acid structures, therefore, it is the job of automated model building software to make this easier for structural biologists. Current software packages such as Buccaneer and ModelCraft can complete this well for proteins, but protein-nucleotides are complex cases which are difficult to automatically build. With the release of AlphaFold 2, there is the opportunity to use the computed AlphaFold structure as a target for molecular replacement and improve the accuracy of atomic models for large complexes. This project is completely computational with the majority of programming in C++ with some Python for data analysis.