# DNA-Binding active residues prediction **URL:** \ **Category:** HADDOCK\ **Created:** [January 11, 2024, 7:20pm UTC](https://ask.bioexcel.eu/t/dna-binding-active-residues-prediction/4760 "2024-01-11T19:20:05Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![ChapepperoniPizza](https://avatars.discourse-cdn.com/v4/letter/c/ce7236/32.png) [@ChapepperoniPizza](https://ask.bioexcel.eu/u/ChapepperoniPizza)\ **Post date:** [January 11, 2024, 7:20pm UTC](https://ask.bioexcel.eu/t/dna-binding-active-residues-prediction/4760/1 "2024-01-11T19:20:05Z")
Hello, I am attempting to predict the active residues involved in a DNA binding protein and generate a TBL restraints file for HADDOCK. Will WHISCY work for this? Even if it is not suitable, I get an error when attempting to use the WHISCY Server and the runs always fail. If anyone has any alternative recommendations for creating a TGL restraints file for DNA binding, I’d be appreciative. The error code can be seen below: # =========================================================================== command: /opt/software/whiscy/whiscy\_setup.py Dimer1.pdb A --alignment Dimer1\_A.phylseq --alignment\_format FASTA exit status: 0 log: whiscy\_setup [INFO] PDB structure with chain A saved to Dimer1\_A.pdb whiscy\_setup [INFO] Atom accessibility calculated to Dimer1\_A.rsa whiscy\_setup [INFO] Surface and buried residues calculated whiscy\_setup [INFO] Protdist calculated whiscy\_setup [INFO] Conversion table file generated whiscy\_setup [INFO] Whiscy setup finished command: /opt/software/whiscy/whiscy\_protocol.sh Dimer1\_A exit status: 0 log: whiscy\_setup [INFO] PDB structure with chain A saved to Dimer1\_A.pdb whiscy\_setup [INFO] Atom accessibility calculated to Dimer1\_A.rsa whiscy\_setup [INFO] Surface and buried residues calculated whiscy\_setup [INFO] Protdist calculated whiscy\_setup [INFO] Conversion table file generated whiscy\_setup [INFO] Whiscy setup finished whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [ERROR] Can not read sequence number whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [ERROR] Can not read sequence number consadjust [ERROR] Conservation file Dimer1\_A.cons does not exist residue\_distance [INFO] Reading conversion table residue\_distance [INFO] Reading PDB structure from Dimer1\_A.pdb residue\_distance [INFO] Residue distances written to Dimer1\_A.rd parasmooth [INFO] Reading input files parasmooth [ERROR] [Errno 2] No such file or directory: ‘Dimer1\_A.acons’ command: /opt/software/whiscy/bin/whiscy2bfactor.py Dimer1\_A.pdb Dimer1\_A\_bfactor.pdb Dimer1\_A.pscons exit status: 1 log: whiscy\_setup [INFO] PDB structure with chain A saved to Dimer1\_A.pdb whiscy\_setup [INFO] Atom accessibility calculated to Dimer1\_A.rsa whiscy\_setup [INFO] Surface and buried residues calculated whiscy\_setup [INFO] Protdist calculated whiscy\_setup [INFO] Conversion table file generated whiscy\_setup [INFO] Whiscy setup finished whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [ERROR] Can not read sequence number whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [ERROR] Can not read sequence number consadjust [ERROR] Conservation file Dimer1\_A.cons does not exist residue\_distance [INFO] Reading conversion table residue\_distance [INFO] Reading PDB structure from Dimer1\_A.pdb residue\_distance [INFO] Residue distances written to Dimer1\_A.rd parasmooth [INFO] Reading input files parasmooth [ERROR] [Errno 2] No such file or directory: ‘Dimer1\_A.acons’ Traceback (most recent call last): File “/opt/software/whiscy/bin/whiscy2bfactor.py”, line 47, in scores = parse\_whiscy\_scores(whiscy\_scores\_file\_name) File “/opt/software/whiscy/bin/whiscy2bfactor.py”, line 21, in parse\_whiscy\_scores with open(file\_name) as input: FileNotFoundError: [Errno 2] No such file or directory: ‘Dimer1\_A.pscons’ ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [January 15, 2024, 3:10pm UTC](https://ask.bioexcel.eu/t/dna-binding-active-residues-prediction/4760/2 "2024-01-15T15:10:59Z")
The issue could be with the dimer. Is it a homodimer? And indeed whisky has not been trained for that. There are other software around for this task, e.g. Pesto (a recent AI model) ---
**Author:** ![ChapepperoniPizza](https://avatars.discourse-cdn.com/v4/letter/c/ce7236/32.png) [@ChapepperoniPizza](https://ask.bioexcel.eu/u/ChapepperoniPizza)\ **Post date:** [January 15, 2024, 3:26pm UTC](https://ask.bioexcel.eu/t/dna-binding-active-residues-prediction/4760/3 "2024-01-15T15:26:59Z")
It is a homodimer, thank you for your quick response. I’ll begin looking into Pesto, and will attempt a run as a monomer instead. Thank you so much.