Abstract
One of the main goals of the BioExcel CoE is the design and development of biomolecular simulation workflows combining the BioExcel key applications (GROMACS, HADDOCK, PMX) to tackle exciting scientific projects. Over the last few years, particular focus has been placed in workflows with predictive power, combining HPC and AI. Developed workflows have been tested in different use cases with an important link to the pharmacological field, demonstrating the predictive power of the BioExcel key applications assisted by HPC workflows. Three different workflows/studies designed as a collaborative project effort from the CoE partners (NBD, IRB, BSC, KTH, MPG) will be briefly presented in this webinar:
* High-throughput prediction of the impact of genetic variability on drug sensitivity and resistance patterns for clinically relevant EGFR mutations from atomistic simulations.
* Large-scale SARS-CoV2 mutation analysis, including a study on the evolutionary path and host-selection mechanism of SARS-CoV-2.
* DNAffinity: A Machine-Learning approach to predict DNA Binding affinities of Transcription Factors.
Presenters
Adam Hospital is a Postdoctoral fellow at the Molecular Modeling and Bioinformatics Unit (MMB) – Institute for Research in Biomedicine in Barcelona (IRB-Barcelona) and research software engineer for the Spanish National Institute of Bioinformatics (INB). From a computer science background, he jumped to the bioinformatics world and got trapped by the fascinating field of structural bioinformatics. He has been involved in scientific projects at IRB and at the Barcelona Supercomputing Center (BSC), and he is currently leading the workflows team in the BioExcel CoE. While working as a bioinformatician, he obtained his PhD in Biotechnology from the University of Barcelona with his thesis “High Throughput Computational Studies of Macromolecular Structure Flexibility”. He has developed a set of public web servers and databases related to macromolecular structure flexibility, including MDWeb, NAFlex and BigNASim.
Federica Battistini is a Postdoctoral fellow in Modesto Orozco group, in the Structural and Computational Biology program of the Institute for Research in Biomedicine (IRB Barcelona). She has the background of a physical computational chemist but she has also worked in the field of biology. – Undergraduate and master degrees in physical inorganic chemistry at the University of Milan, Italy. – PhD in physical organic chemistry and computational chemistry at the University of Sheffield, UK, under the supervision of Prof. Christopher A. Hunter. Her principal research project involved a theory based approach to understand sequence effects on nucleosome positioning in chromatin. In the current position as a postdoctoral researcher since 2010 she has focused her research on the study of nucleic acid dynamics at the molecular level and the sequence effects on the physical and chemical properties of these biomolecules as well as epigenetic effects. She has been involved in projects at IRB and Barcelona Supercomputing Center (BSC) and collaborated in building programs and databases related to DNA protein-recognition and flexibility.
Miłosz Wieczór is currently a Marie Skłodowska-Curie Post-Doctoral Fellow, working in the Molecular Modelling and Bioinformatics group headed by Prof. Modesto Orozco in Barcelona’s Institute for Research in Biomedicine (IRB). He recently earned his PhD from Gdańsk University of Technology working on the interactions between telomeric DNA and proteins with simulational tools, mostly focusing on the application of state-of-the-art free energy methods with classical or quantum/classical computational models. Alongside, he contributed to numerous projects covering a range of topics from nanomechanics to biomembranes to protein-ligand interactions, which prompted his general interest in programming and scientific visualization. His current work remains centered around nucleic acids, primarily addressing the relationships between DNA damage and epigenetics, mechanics of nucleosome positioning, and development of tools for the improvement of classical force fields.
Register for webinar
Title: BioExcel HPC Workflows: predictive power and its applications in pharmacology.
Date: April 26, 2022
Time: 15:00 CEST
Slides URL: https://zenodo.org/record/6512154#.YnE-GpLMJpQ
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