A Few Words About Us
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
In silico
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.
In vitro
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.
Outreach
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.
Open source
Get the code / visit our repo at :
Publications & Conferences
During CYBORG implementation
2023
Conferences
Laurențiu Spiridon, Teodor Asvadur Şulea, Victor Gabriel Ungureanu, Eliza Cristina Martin, Andrei Jose Petrescu, “Explorarea complexelor biomoleculă-medicament prin prisma mecanicii roboților”, Farmacia azi: de la tradiție la interdisciplinaritate și inteligență artificială, Septembrie 2023, Cluj-Napoca, Romania.
Victor Gabriel Ungureanu, Ioana Popa, Carmen Tănase, Laurențiu Spiridon, “In-silico Study of RAGE-S100B Inhibitors”, Studia Universitatis Babeș-Bolyai, Biologia, 68(2), December 2023, The Annual International Conference of the RSBMB, Cluj-Napoca, Romania
Laurentiu Spiridon, Teodor Asvadur Şulea, Victor Gabriel Ungureanu, Eliza Cristina Martin, Andrei Jose Petrescu, “Robosample: Harnessing the power of constrained molecular dynamics and Gibbs sampling to investigate macromolecules”, Studia Universitatis Babeș-Bolyai, Biologia, 68(2), December 2023, The Annual International Conference of the RSBMB, Cluj-Napoca, Romania
Spiridon L, Sulea TA, Ungureanu VG, Martin EC, Minh DDL, “Robosample: A software using constrained molecular dynamics coupled with Gibbs sampling to investigate macromolecules.”, Biophysical Journal, 122 (3), sup 1, 177A, February 10, 2023, 67th Biophysical Society Annual Meeting, San Diego, CA, USA
Scientific Report Summary 2023 - download PDF
Papers
Chiriţoiu GN, Munteanu CVA, Şulea TA, Spiridon L, Petrescu AJ, Jandus C, Romero P, Petrescu ŞM. “Methionine oxidation selectively enhances T cell reactivity against a melanoma antigen. iScience.” 2023 (IF=6.3)
2022
Conferences
Teodor A. Şulea, Eliza C. Martin, Victor G. Ungureanu, Andrei J. Petrescu, Laurentiu Spiridon. “Highly Efficient Exploration of Conformational Spaces using Robot Mechanics - A Helical Bundle Case Study”. Conferința Joint 25th IUBMB, 46th FEBS, and 15th PABMB Congress, Talks. FEBS Open Bio, Lisabona, Portugalia, 9-14 iulie 2022.
Teodor A. Şulea, Victor G. Ungureanu, Eliza C. Martin, Andrei-Jose Petrescu, Laurențiu Spiridon: “Robosample: A Molecular Simulation Program That Combines Enhanced Sampling with High-Speed Robotics Algorithms”. New Trends And Strategies In The Chemistry Of Advanced Materials With Relevance In Biological Systems, Technique And Environmental Protection, Timișoara, România, 20-21 octombrie 2022.
Scientific Report Summary 2022 - download PDF
2021
Conferences
Teodor A. Şulea, Victor G. Ungureanu, Eliza C. Martin, Andrei J. Petrescu, Laurentiu Spiridon. “Robosample - platforma de noua genaratie pentru eșantionarea spațiilor conformaționale ale biomoleculelor”. Conferința Cercetării Științifice din Academia Română (CCSAR-2021). Academia Romana, Bucureşti, 22-23 noiembrie 2021.
Teodor A. Şulea, Eliza C. Martin, Victor G. Ungureanu, Laurențiu Spiridon, Andrei-Jose Petrescu: “ROBOSAMPLE: robotics-based Gibbs sampling of macro-molecular systems”. MacroYouth2021 Scientific Communications of Young Researchers, Iasi, 19 noiembrie 2021.
Scientific Report Summary 2021 - download PDF
Anterior group results
Representing the foundation on which CYBORG project work commenced
Spiridon L, Şulea TA, Minh DDL, Petrescu AJ. "Robosample: A rigid-body molecular simulation program based on robot mechanics." Biochim Biophys Acta Gen Subj. 1864(8), 129616, 2020 (IF=3.68)
Spiridon L, Minh DDL. “Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.” J Chem Theory Comput. 13:4649-4659, 2017 (IF=6.07)
Team
Laurentiu Spiridon
Project Manager
Victor G. Ungureanu
Software Engineer & Medical school student
Teodor A. Sulea
Ph.D.student in Bioinformatics
Laura Manoliu
Ph.D.student in Bioinformatics
Eliza Martin
Ph.D.student in BioinformaticsFunding
Contact
Splaiul Independentei 296,
Bucharest, Romania
+4 021 223 90 69
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