This project aims to improve protein engineering for medical and food security applications by leveraging advanced in silico assistance. Our software, Robosample, combines robotics algorithms with Gibbs sampling to accurately recover biomolecular free energy surfaces. We will further integrate robotics and molecular simulation by introducing new non-equilibrium sampling methods and novel robotic joints.
New biological entity development - protein engineering for medical or food security applications is extremely lengthy and costly and better in sillico assistance is paramount. For this purpose, our software - Robosample combines the speed of robot mechanics algorithms with Gibbs sampling to recover the correct free energy surfaces of biomolecules
This project is based on my work within the Illinois Institute of Technology as well as during the previous UEFISCDI TE2016 project. We propose a deeper merge between robotics and molecular simulation by introducing non-equilibrium sampling methods and new types of robotic joints never tried for molecules for which we have very promising preliminary data – for example we had a 6 times fold increase in folding time of extended deca-alanine into an α-helix.
We also aim to perform experimental work driven by our simulation analysis. Experimental work will involve novel antigenic peptide testing for melanoma immunotherapy using our Nano LC - MS System - Orbitrap Velos Pro System and HCV NS2-NS3 structure investigation through mutations. Assistance for experimental work will be provided for various partners in the following hot topics in molecular biosciences: plant-pathogen interaction.
The project also aims to make the software accessible to a wider scientific community. This will allow research groups focus more on analysis and less on implementation.
Laurentiu Spiridon is a researcher in the Institute of Biochemistry of the Romanian Academy. Laurentiu is currently working in Bioinformatics & Structural Biochemistry in the Bioinformatics & Structural Biochemistry.
The project aims at developing Robosample up to an established software in the world of molecular simulation by proving its efficacy in assisting bio-molecular experimental work such as bio-medical and food safety related applications.
Also, the project aims at a better fusion between molecular simulation techniques and robot mechanics meaning non-equilibrium sampling methods and new types of robotic joints as well as refactor the code for speed.
Laurentiu Spiridon – Principal Investigator
Eliza-Cristina martin – PhD Student
Teodor Asvadur Sulea – PhD Student
Victor Gabriel Ungureanu - Student
Cristian Munteanu – Scientific Researcher
Gabriela Chiritoiu – Scientific Researcher
Costin-Ioan Popescu – Senior Scientific Researcher
Floriana Siebel Bectas – PhD Student
In regard to methods development the project achieved improved model system folding times for new types of robotic joints simulations and improved model system kinetic rates improvement for non-equilibrium Hamiltonian Monte Carlo simulations. Robosample software capabilities were increased by adding third party software external communication modules, refactorization for speed improvement and increased user accessibility.
Romanian Academy