Modeling protein-small molecule conformational ensembles with PLACER.

ABSTRACT: Modeling the conformational heterogeneity of protein-small molecule interactions is important for understanding natural systems and evaluating designed systems, but remains an outstanding challenge. We reasoned that while residue level descriptions of biomolecules are efficient for de novo structure prediction, for probing heterogeneity of interactions with small molecules in the folded state an entirely atomic level description could have advantages in speed and generality. We developed a graph neural network called PLACER (Protein-Ligand Atomistic Conformational Ensemble Resolver) trained to recapitulate correct atomic positions from partially corrupted input structures from the Cambridge Structural Database and the Protein Data Bank; the nodes of the graph are the atoms in the system. P

SUBMITTER: Anishchenko I 

PROVIDER: S-EPMC11463446 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature