Zhanglab forum

Yes, you can use COACH to predict the active site of a protein by providing a docked model in PDB format. COACH is a meta-server that analyzes the 3D structure of a protein to identify potential ligand-binding sites, including active sites. It utilizes comparative methods like TM-SITE and S-SITE ...

In protein structure prediction and modeling, restraint files such as comb.dat, geometry dash comb8CA.dat, combCA.dat, dist.dat, distL.dat, and par.dat are crucial for guiding the modeling process by incorporating information from threading templates. These files are typically generated by scripts ...

The error message indicates that I-TASSER is having trouble recognizing your input sequence length,fireboy and watergirl which it claims is outside the acceptable range of 10 to 1500 residues. However, your sequence is only about 70 residues long, which is within this range.

There is no direct option in I-TASSER to include all protons during the prediction process,dinosaur game as I-TASSER focuses on heavy atom positioning for peptide backbones and side chains. Therefore, post-processing with external software is necessary to include all protons.