# Active residue prediction **URL:** \ **Category:** HADDOCK\ **Created:** [May 12, 2025, 9:54pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667 "2025-05-12T21:54:39Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Post date:** [May 12, 2025, 9:54pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/1 "2025-05-12T21:54:40Z")
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. ---
**Author:** ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko)\ **Post date:** [May 13, 2025, 7:10am UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/2 "2025-05-13T07:10:42Z")
In prinsiple, you can start with the literature search - see if there’s any experimental data awaliable. If so, you may not need to make any predictions. You can also use [ARCTIC-3D](https://rascar.science.uu.nl/arctic3d/) for an actual prediction. For WHISCY, you can obtain an aligmenet for you protein using BLAST. Check out this tutorial [Structural Bioinformatics & Modelling – Bonvin Lab](https://www.bonvinlab.org/education/molmod_online/). The part on homology modelling can help you with the BLAST, the part on docking - with ARCTIC-3D. ---
**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:** [May 13, 2025, 7:44am UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/3 "2025-05-13T07:44:28Z")
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 ---
**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Post date:** [May 14, 2025, 5:04pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/4 "2025-05-14T17:04:21Z")
Thank you for your guidance. ---
**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Post date:** [May 14, 2025, 5:09pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/5 "2025-05-14T17:09:08Z")
Thank you. I am experiencing issues with the “ARCTIC-3D” and “WHISCY” 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? ---
**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:** [May 14, 2025, 8:55pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/6 "2025-05-14T20:55:42Z")
What is your input for Arctic3D? ---
**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Post date:** [May 14, 2025, 10:17pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/7 "2025-05-14T22:17:57Z")
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.** ---
**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:** [May 15, 2025, 7:10am UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/8 "2025-05-15T07:10:51Z")
this must mean there is no info about interactions from the PDB for this protein ---
**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Post date:** [May 15, 2025, 8:08am UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/9 "2025-05-15T08:08:35Z")
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](https://pesto.epfl.ch/) to predict potential interacting residues ---
**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Post date:** [May 27, 2025, 9:32pm UTC](https://ask.bioexcel.eu/t/active-residue-prediction/5667/10 "2025-05-27T21:32:15Z")
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 list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… 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 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 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 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 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 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 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 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 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: ‘model\_01\_1\_B.acons’ 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 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 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: ‘model\_01\_1\_B.acons’ Traceback (most recent call last): File “/usr/local/bin/whiscy\_bfactor”, line 6, in sys.exit(main()) ^^^^^^ File “/opt/software/whiscy/src/whiscy/cli\_bfactor.py”, line 68, in main scores = parse\_whiscy\_scores(whiscy\_scores\_file\_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/opt/software/whiscy/src/whiscy/cli\_bfactor.py”, line 31, in parse\_whiscy\_scores with open(file\_name) as input: ^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: ‘model\_01\_1\_B.pscons’. Please guide me through this.