The basic instructions to compute the KORP energies for both loops and proteins are described here. At download section you can get the latest version and several benchmarks compiled for testing the performance in protein and loop modeling scenarios.
The KORP energy computation for protein model is fast and easy with "korpe"
In this case just provide a PDB file of the protein and the corresponding energy map. For example, in directory CASP12DCsel20/ run:
The computed energy will be prompted to screen
For a multiple cases just input a plain text file with the basenames of the PDBs, i.e. a list of PDB file names without the .pdb extension. As an example, in directory CASP12DCsel20/ you can run:
Tips & tricks
- Check the path of the energy map file korp6Dv1.bin.
- Use a correct residue numeration in the PDB, it may be important for bonding/non-bonding contacts discrimination
- KORP energy is side-chain independent, it only requires the coordinates of the N, CA, and C atoms.
The KORP energy computation for loop ensembles is fast and easy with "korpe"
For a single case run, just provide a PDB file (filaname.pdb) of the protein and a Multi-PDB file with all the loops to be assessed (multi_loops.pdb)
In the output basename.txt file you will find a table with the KORP energies.
For example in the directory rcd6/ you can run:
and check the 3CXM_result.txt file.
For a multiple cases run, use a plain text file with the base names of the protein PDBs, i.e. a list of PDB file names without the .pdb extension (filename_list.txt), and the common suffix of the loops Multi-PDB files (_loops.pdb) instead.
For each XXX entry in the filename_list.txt you will find a file name XXX_suffix.txt with the corresponding a table with the KORP energies.
For example, in the directory rcd6/ you can run:
Tips & tricks
- The presence of one N-terminal and one C-terminal residue (anchors) in the Multi-PDB file is mandatory
- Both the protein PDB and the loops Multi-PDB must be numerated consistently
- Check the path of the energy map file korp6Dv1.bin
- KORP energy is side-chain independent, it only requires the coordinates of the N, CA, and C mainchain atoms. You can save reading time by input only N,CA,C pdb files.
- If benchmarking, add the --rmsd flag and provide a complete PDB (with nativeloop) to obtain complete KORP energy statistics in the output_score.txt file. For example, use these commands for single and multiple runs, respectively:
Please, cite our work if our tools or benchmarks become useful for your research.
KORP energy and benchmarks
- López-Blanco JR and Chacón P (2018). KORP: Knowledge-based 6Dpotential for protein structure prediction. (submitted)
Improved RCD method
- López-Blanco JR, Canosa-Valls AJ, Li Y, and Chacón P (2016). RCD+: Fast loop modeling server. NAR (DOI: 10.1093/nar/gkw395)