How much does 3D molecular modelling software cost?
Introduction 3D molecular modelling plays a vital role in modern drug discovery, offering powerful applications to streamline research, reduce costs,…
Abstract
Macrocyclic peptides are an important modality in drug discovery, but molecular design is limited due to the complexity of their conformational landscape. To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures.
Unexpectedly large strain energies were observed when the bound-state conformations were modeled with positional restraints. Instead, low-energy conformer ensembles were generated using xGen that fit experimental X-ray electron density maps and gave reasonable strain energy estimates. The ensembles featured significant conformational adjustments while still fitting the electron density as well or better than the original coordinates.
Strain estimates suggest the interaction energy in protein–ligand complexes can offset a greater amount of strain for macrocyclic peptides than for small molecules and non-peptidic macrocycles. Across all molecular classes, the approximate upper bound on global strain energies had the same relationship with molecular size, and bound-state ensembles from xGen yielded favorable binding energy estimates.
More publications to browse
What are the best AI drug discovery software platforms?
What value does AI offer in drug discovery? The potential is huge: To learn more about the value we’re seeing…
Will AI replace chemists?
ChatGPT can be great for the basics, but cannot replace expert human knowledge I’m going to quickly discount the most…
