Need advice! I performed homology modeling using HHpred with two approaches:
1) Local alignment. I selected all 20 templates generated. [Note: all the templates only cover the query sequence from residue 150 onwards though].
2) All options are as default, except using global alignment [to obtain templates in fragments for residue 1 - 150, and the rest of the query sequence, in total of 20 templates].
I then performed energy minimization using Gromacs. And then Procheck for validation. For the first approach, there are some error such as:
- Ramachandran plot: 90.1% core 7.0% allow 1.8% gener 1.0% disall
- All Ramachandrans: 18 labelled residues (out of 571)
- Residue properties: Max.deviation: 4.4 Bad contacts: 18 * Bond len/angle: 8.5 Morris et al class: 1 1 2 G-factors Dihedrals: -0.02 Covalent: -0.33 Overall: -0.13
- M/c bond angles: 91.8% within limits 8.2% highlighted 1 off graph
For the second approach, there was a warning:
- Warning: fopen(/var/www/html/Services/SAVES3/jobs/483990/procheck/protein.sum) [function.fopen]: failed to open stream: No such file or directory in /var/www/html/Services/SAVES3/utils.php on line 145 Cannot PROCHECK find or open: /var/www/html/Services/SAVES_3/jobs/483990/procheck/protein.sum
My question is, can I still proceed with further analysis such as protein docking to study its binding site and all for the protein generated in the first approach (with the error and all, plus, the residues from 1 - 150 were constructed without homology). And why is there a warning for the validation for the second approach when I randomly select the templates for the global alignment mode?
Please advice. Thanking you all in advance! :)