Publications – Page 2 – BioExcel – Centre of Excellence for Computation Biomolecular Research

Below is a list of related publications by the partners of the BioExcel consortium. We strive to publish as Open Access, or to provide green open access preprints where gold open access is not possible. Please let us know if you are unable to access any of our publications.

These pages lists publication in reverse chronological order, see also the full list of pulications for citation information.

Comparison of experimentally measured and calculated binding affinities for PTP1B protein-ligand system

Automated relative binding free energy calculations: from SMILES to ΔΔG

August 25, 2022November 3, 2022Stian Soiland-Reyes

In drug discovery, computational methods are a key part of making informed design decisions and prioritising compounds. In particular, optimizing compound affinity is [...]

Distributions of the λ-coordinate (A, E) and dihedrals (B-D, F-H) in constant pH MD simulation of Asp with the original (A-D) and modified CHARMM36m (E-H) force field

Best practices in constant pH MD simulations: accuracy and sampling

August 18, 2022November 3, 2022Stian Soiland-Reyes

Various approaches have been proposed to include the effect of pH in Molecular Dynamics (MD) simulations. Among these, the lambda-dynamics approach proposed by [...]

Oligomerization and membrane remodelling

Teixobactin kills bacteria by a two-pronged attack on the cell envelope

August 3, 2022November 3, 2022Stian Soiland-Reyes

Antibiotics that use novel mechanisms are needed to combat antimicrobial resistance. Teixobactin represents a new class of antibiotics with a unique chemical scaffold [...]