covid-19 – BioExcel – Centre of Excellence for Computation Biomolecular Research

Figure 2: aforementioned local transmission clusters in Lithuania, Spain (Vilassar De Mar, province of Barcelona), France (see below), and Germany (state of Bavaria), amongst numerous others

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

September 5, 2022September 5, 2022Stian Soiland-Reyes

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here [...]

Pre-Exascale HPC-approaches for Molecular Dynamics simulations. Covid-19 research: a use case

May 30, 2022July 4, 2022Stian Soiland-Reyes

Exascale computing has been a dream for ages and is close to become a reality that will impact the way in which molecular simulations are being performed and the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis in recent work from groups in the BioExcel Center of Excellence for High Performance Computing. [...]

Evolutionary Path and Host-selection Mechanism of SARS-CoV-2

May 18, 2022July 4, 2022Stian Soiland-Reyes

Here, through massive plain MD simulations, enhanced sampling calculations, free energy-based alchemical transformation and bioinformatics we show that SARS-CoV-2 likely evolved in Rhinolophus affinis bats by acquiring a surprisingly-high affinity for their ACE2 receptors. [...]

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

January 13, 2022April 13, 2022Stian Soiland-Reyes

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. [...]