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When I try to install PRODIGY by pip, it looks like something went wrong

minfei@minfei:~$ pip install prodigy
Defaulting to user installation because normal site-packages is not writeable
ERROR: Could not find a version that satisfies the requirement prodigy (from versions: none)
ERROR: No matching distribution found for prodigy

(...) it seems that the code does not accept any spaces or "-" in the file name.

Originally posted by @esraaelmligy in #16 (comment)

Hello,

I'm currently running prodigy on a protein complex.
I don't see any changes in the terminal or in the directory when activating the contact_list flag

Do you have any idea why?

(prodigy) loris@big-gpu:~/dev/prodigy$ prodigy 7f62.pdb --selection H,L A
[+] Reading structure file: /home/loris/loris/ground_thruth/7f62.pdb
[!] Structure contains gaps:
        A PRO330 < Fragment 0 > A LYS444
        A GLY447 < Fragment 1 > A SER530
        H GLU1 < Fragment 2 > H ALA119
        L GLN1 < Fragment 3 > L ARG109
[+] Parsed structure file 7f62 (3 chains, 427 residues)
.....
[++] Predicted binding affinity (kcal.mol-1):    -11.5
[++] Predicted dissociation constant (M) at 25.0˚C:  3.6e-09

(prodigy) loris@big-gpu:~/dev/prodigy$ prodigy ground_thruth/7f62.pdb --selection H,L A **--contact_list**
[+] Reading structure file: /home/loris/loris/ground_thruth/7f62.pdb
[!] Structure contains gaps:
        A PRO330 < Fragment 0 > A LYS444
        A GLY447 < Fragment 1 > A SER530
        H GLU1 < Fragment 2 > H ALA119
        L GLN1 < Fragment 3 > L ARG109
[+] Parsed structure file 7f62 (3 chains, 427 residues)
....
[++] Predicted binding affinity (kcal.mol-1):    -11.5
[++] Predicted dissociation constant (M) at 25.0˚C:  3.6e-09
(prodigy) loris@big-gpu:~/dev/prodigy$ 

Several users have asked for help relating to this error message Radius array is <= 0 for the residue: ILE ,atom: CD

1. https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375
2. https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835
3. https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825
4. https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420
5. https://ask.bioexcel.eu/t/some-problems-in-doing-prodigy/3187

This message specifically seems related to a input structure containing atoms other than CD - which might be the case for structures generated with a few different modelling software.

We could improve the message to already contain the advice on how to proceed;

[!] Error: Radius array is <= 0 for the residue: ILE ,atom: CD
[!] Error: Make sure the atom names in your PDB file match the cannonical naming and belong to default residues

Keeps giving me this error for the pdb file argument and i don't really know why

Hello,
I was wondering how to interpret the results of a complex.

[+] Parsed structure file 7F62_input_fasta_relaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000 (3 chains, 427 residues)
[+] No. of intermolecular contacts: 55
[+] No. of charged-charged contacts: 3
[+] No. of charged-polar contacts: 8
[+] No. of charged-apolar contacts: 12
[+] No. of polar-polar contacts: 5
[+] No. of apolar-polar contacts: 16
[+] No. of apolar-apolar contacts: 11
[+] Percentage of apolar NIS residues: 35.60
[+] Percentage of charged NIS residues: 19.50
[++] Predicted binding affinity (kcal.mol-1): -10.7
[++] Predicted dissociation constant (M) at 25.0˚C: 1.3e-08

Is the binding affinity score made up of all the "[+]" scores ?

Dear Authors,

Thanks so much for the amazing work.

I am a PhD student at Eotvos Lorand University looking for the dataset provided in the paper: Kastritis P. L., Moal I. H., Hwang H., Weng Z., Bates P. A., Bonvin A. M. and Janin J.(2011). A structure-based benchmark for protein-protein binding affinity.

I wanted to know if its still available and if not, what open-source dataset/s you would suggest with affinity data as well as 3D bound structures?

All the best,
Oz

Hi,

Thank you for making this wonderful tools.
I was trying this command:

prodigy my_input.pdb --selection A B --pymol_selection

It prints the output.
But I couldn't find the Pymol script. What's the way to resolve it?

G.V.

Hi, I encountered this error after running prodigy on some PDB ids (eg. 1TVD, 4E44, 2PUX).
Seems that some residue numbers are not integers for some reason.

Demo code:
I am using python3_package branch.

> prodigy 1TVD.pdb  --selection A B --contact_list --pymol_selection 
[+] Reading structure file: 1TVD.pdb
[!] Structure contains gaps:
        A ASP1 < Fragment 0 > A GLY57
        A GLY58 < Fragment 1 > A PRO116
        B ASP1 < Fragment 2 > B GLY57
        B GLY58 < Fragment 3 > B PRO116

[+] Parsed structure file 1TVD (2 chains, 226 residues)
Traceback (most recent call last):
  File "prodigy", line 11, in <module>
    load_entry_point('prodigy', 'console_scripts', 'prodigy')()
  File "prodigy/prodigy/predict_IC.py", line 311, in main
    prodigy.predict(distance_cutoff=cmd.distance_cutoff, acc_threshold=cmd.acc_threshold)
  File "prodigy/prodigy/predict_IC.py", line 146, in predict
    _, cmplx_sasa = execute_freesasa_api(self.structure)
  File "prodigy/prodigy/lib/freesasa_tools.py", line 185, in execute_freesasa_api
    resid = int(struct.residueNumber(idx))
ValueError: invalid literal for int() with base 10: '57B'

I wonder if there is any easy way to get around this error.

When using the attached pdb file, prodigy silently fails in the server with the following message:

[!] Structure contains gaps:
A ASP1 < Fragment 0 > A THR186
A LEU187 < Fragment 1 > A LEU286
A LEU287 < Fragment 2 > A GLN425
A MET426 < Fragment 3 > A SER551
B CYS552 < Fragment 4 > B CYS567

Running Prodigy for structure test
ERROR:

test.pdb.zip

Just a minor issue - versions 2.1.4 and 2.1.5 of prodigy are both listed as v2.1.3 when running prodigy -V on the command line, and is also listed as v2.1.3 by pip after installation. For pip, can this be fixed by bumping the version number in pyproject.toml on line 4? For the command line, it looks like the version is controlled by line 19 of prodigy/predict_IC.py.

Hi, I encountered this error after running prodigy on some PDB ids (eg. 4JGJ, 4H10, 4XRS).
Seems that some residue names are non-standard for some reason.

Demo code:
I am using python3_package branch.

> prodigy 4XRS.pdb  --selection A G --contact_list --pymol_selection
[+] Reading structure file: 4XRS.pdb
Traceback (most recent call last):
  File "prodigy", line 11, in <module>
    load_entry_point('prodigy', 'console_scripts', 'prodigy')()
  File "prodigy/prodigy/predict_IC.py", line 308, in main
    structure, n_chains, n_res = parse_structure(struct_path)
  File "prodigy/prodigy/lib/parsers.py", line 141, in parse_structure
    return (validate_structure(s),
  File "prodigy/prodigy/lib/parsers.py", line 87, in validate_structure
    raise ValueError('Unsupported non-standard amino acid found: {0}'.format(res.resname))
ValueError: Unsupported non-standard amino acid found:  DC

I wonder if there is any easy way to get around this error.

Hi again,
A quick question: Would it be possible to calculate binding affinity for a defined section of the interface e.g. protein domain, with the method used by prodigy?
It seems that prodigy (in its current version) is designed to estimate the binding affinities for entire binding interface. Out of curiosity, I wonder if there any possibility that this method could be used to obtain domain-wise binding affinities.
Thanks.

I believe that the --acc-threshold parameter specifies the accessibility threshold for the buried surface area analysis. Is this parameter a percentage? I tried changing the default from 0.05 to 1.25 and it worked, but anything larger failed.

My thought is that the IC contact list might help me with the TAP criteria. Would the IC residues be similar to the "CDR vicinity" in the TAP calculations?