realbigws / deepalign Goto Github PK

Hello,

I would like to use DeepAlign_Search.sh to perform structure search against PDB.
However, I have some questions about the database used by DeepAlign:

First, how can I download the DB?

According to the README,

Users can download some protein structure databases from http://raptorx.uchicago.edu/download/
(...)
2. PDB database
If databases/pdb_BC100/ does not exist, create one.
Copy or link all the .pdb files to databases/pdb_BC100/

But, where can I find pdb_BC100?
There are only pdb_BC40_20210204.tar.gz and pdb_Remain_20210204.tar.gz at http://raptorx.uchicago.edu/download/.

Second, how DBs were constructed?

How did you process the raw PDB files to obtain pdb_BC40_20210204.tar.gz?
I believe that you normalized the raw PDB files using the tools under util/ and clustered them with >40% identity in some way. Is this correct understanding? If so, where can I refer to for the procedure?

Thanks for answering.
Best,
mt

Hello, I have a question. Do you know how to calculate tmscore for two fragment of protein. I mean that i want to use the global align matrix calculated by the complete protein structures.

After running 3DCOMB, how do I find out to which input structure each segment/chain of the aligned structures correspond?
Thanks!

downloaded the build, make file fails because of broken links in the source code. May be worth revisiting, found an older build which compiles fine.