Hello
I would like to perform protein-protein docking using HADDOCK webserver, but I do not know what is the interface of these two proteins, and I do not know what are the active residues of them. How can I predict that? Also, when I use WHISCY, it requires to insert alignment file, but I do not have it.
Please guide me through this issue.
In prinsiple, you can start with the literature search - see if thereās any experimental data awaliable. If so, you may not need to make any predictions.
You can also use ARCTIC-3D for an actual prediction.
For WHISCY, you can obtain an aligmenet for you protein using BLAST. Check out this tutorial Structural Bioinformatics & Modelling ā Bonvin Lab. The part on homology modelling can help you with the BLAST, the part on docking - with ARCTIC-3D.
And to add some more information, you could run haddock in ab-initio mode, using for example centre-of-mass restraints (does require expert level access).
But HADDOCK is at its best when you can provide some information.
You might also consider using other docking servers for this
Thank you for your guidance.
Thank you. I am experiencing issues with the āARCTIC-3Dā and āWHISCYā webservers. I receive an internal server error when using ARCTIC-3D, and WHISCY does not display any processing or results.
Can you please guide me though this?
What is your input for Arctic3D?
I am only inserting a UniProt ID as an input. Currently it is not giving error, but it is written: No cluster information could be obtained for this job.
this must mean there is no info about interactions from the PDB for this protein
In that case, you can query arctic-3d with a (several) closely related homolog(s) and map back the interacting residues.
An other approach would be to use PeSTo to predict potential interacting residues
Thank you for your guidance. I am still trying to use WHISCY webserver, but when I insert my alignment file (FASTA or .aln format), I am getting error: Run 3+r48DDe
Status: FAILED
See the error output below which might include an indication about why your run failed. If you need assistance please reach us out at ask.bioexcel.eu
command: whiscy_setup model_01_1.pdb B --alignment rcsb_pdb_4RZK.fasta --alignment_format FASTA
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
command: whiscy model_01_1_B.sur model_01_1_B.conv model_01_1_B.phylseq model_01_1_B.out -o model_01_1_B.cons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
command: whiscy model_01_1_B.lac model_01_1_B.conv model_01_1_B.phylseq model_01_1_B.out -o model_01_1_B.lcons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
command: whiscy_consadjust model_01_1_B.cons -o model_01_1_B.acons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
command: whiscy_resdist model_01_1_B.pdb model_01_1_B.conv model_01_1_B.rd
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from model_01_1_B.pdb
residue_distance [INFO] Residue distances written to model_01_1_B.rd
command: whiscy_parasmooth model_01_1_B.acons model_01_1_B.lcons model_01_1_B.rd -o model_01_1_B.pscons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from model_01_1_B.pdb
residue_distance [INFO] Residue distances written to model_01_1_B.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: āmodel_01_1_B.aconsā
command: whiscy_bfactor model_01_1_B.pdb model_01_1_B_bfactor.pdb model_01_1_B.pscons
exit status: 1
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface listā¦
whiscy [INFO] Loading conversion tableā¦
whiscy [INFO] Convertingā¦
whiscy [INFO] Initializing score calculationā¦
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from model_01_1_B.pdb
residue_distance [INFO] Residue distances written to model_01_1_B.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: āmodel_01_1_B.aconsā
Traceback (most recent call last):
File ā/usr/local/bin/whiscy_bfactorā, line 6, in
sys.exit(main())
^^^^^^
File ā/opt/software/whiscy/src/whiscy/cli_bfactor.pyā, line 68, in main
scores = parse_whiscy_scores(whiscy_scores_file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ā/opt/software/whiscy/src/whiscy/cli_bfactor.pyā, line 31, in parse_whiscy_scores
with open(file_name) as input:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: āmodel_01_1_B.psconsā. Please guide me through this.