I was working on a PDB structures with 3 missing loops. Two of them have more than 15 missing residues. In this case, are the loop modeling methods still applicable? If so, which algorithm should I follow? Can I ask if there is a better way to fill the loops without affecting the existing region in the PDB structure? Thank you!
Next gen KIC has been benchmarked on longer loops, see https://doi.org/10.1371/journal.pone.0063090 - a little more than 15 residues may work, but you will likely need a lot of iterations to find a good low-scoring conformation. Depending on the modelling task you are planning, it may also be possible to work without reconstructing the loops.
Thank you for the information! I was also thinking about using RosettaCM to build homology models with similar proteins to fill the missing regions, but how can I keep the existing regions in the PDB structure unchanged?