The three-dimensional structures of biological macromolecules are the starting point for molecular-level studies.
We have worked on the accurate modeling of protein structures since CASP4. A key contribution has been the refinement of homology models via physics-based molecular dynamics simulations.
Since the advent of AlphaFold, we have shifted our interest to the modeling of conformational ensembles focusing on:
- predictions of state-specific structures
- dynamic ensembles consistent with experimental data
- generative modeling of conformational landscapes
Software and modeling resources:
- alphafold-multistate: state-specific modeling using AlphaFold
- asam: generative modeling of conformational ensembles
Published structures:
- 8W0Q: Dynamic loop ensemble of a CDR-H3 antibody mimic
