ProtClean Updates & Roadmap
Upcoming
Integration with OMP for greater ease of downloading and preparing membrane-bound receptors
Initial release (v1.0.0)
AI-powered loop patching
- Based on AlphaFold, modified for the purpose of patching loops on existing, known crystal structures. Missing loops are given coordinates with minimal changes to the residues that already had them.
- Patching missing loops, more accurately than traditional approaches, provides complete structures and more accurate results with other modules like QUELO.
Membrane generation and equilibration
- Embeds uploaded protein into the pre-equilibrated, fully atomistic membrane and equilibrates through solvent box expansion and contraction. Upload target aligned along the z-axis and can visualize and adjust the position of the target within the membrane. Many common membranes to choose from, including popc, dlpe, and dopc.
- Much faster membrane equilibration, achieving what is typically done in days (or even weeks) in just a few hours.
Select chains and cofactors to retain and exclude from cleaned PDB, with full 3D visualization of where they are