There are well-known solutions such as AlphaFold for predicting 3D DNA structures. 3D RNA structures are less examined and therefore there are not yet good quality preditors for them. There are contests, such as CASP, in which mathematical models and scientists compete for best 3D RNA prediction from a sequence. Our goal was to prepare a deep learning model that could assess the quality of predicted structures. In our batchelor thesis, we proposes a Graph Attention Network for this purpose. A simmilar approach had been taken by a team that proposed the "ARES" structure atom-level model. We tried to achieve better performance by involving a residue-level model containing angular features and their relationships.
https://github.com/adamczykb/rnaquanet Download thesis09 Febuary 2024
WebTetrado is a web server for analyzing 3D structures of quadruplex structures. It has a user-friendly interface and offers many advanced features, including automatic identification, annotation, classification, and visualization of the motif. The program applies to the experimental or in silico generated 3D models provided in the PDB and PDBx/mmCIF files. It supports canonical G-quadruplexes as well as non-G-based quartets. It can process unimolecular, bimolecular, and tetramolecular quadruplexes.
doi.org/10.1093/nar/gkad34609 May 2023
RNAsolo is a self-updating database dedicated to RNA bioinformatics. It systematically collects experimentally determined RNA 3D structures stored in the PDB, cleans them from non-RNA chains, and groups them into equivalence classes. It allows users to download various subsets of data clustered by resolution, source, data format, etc. for further processing and analysis with a single click.
doi.org/10.1093/bioinformatics/btac38608 June 2022
At AgroOsa, I am responsible for developing a new dedicated Linux-based system for controlling autonomous agricultural equipment. The system is being builded using Qt framework and OpenGL low-level visualisation. My responsibilities include also server-site developing and maintanance.
June 2023 - present
I was involved into a scientific project aimed on exploring quadruplexes in RNA 3D structures. During the time I developed two tools that was published in prestigious journals. I learned a lot about data processing, building pipelines and good coding practises. I was responsible for introducing two persons to data analysis and web applications development. Moreover I was presenting my work on four international conferences.
March 2021 - present
As an intern, I was responsible for extending functionality of the company's main project "CasuSoft". I gain experience in developing large business projects and scrum project methodology.
July-August 2020,2021
As an intern, I got a challange to develop e-commerce platform for that company. Main goal was to integrate payment system for subscription and serving licence keys for their services. During summer internship I was delegated to upgrade one of company's project dependecies.
March 2019, July 2019
During my first summer internship, I was responsible for maintaining and administering the company's ERP system. During second summer, I was only person in charge of the system.
July-August 2017,2018