PRODIGY(1)

💖 PRODIGY 💖

okay bestie, gather round, because prodigy (that's the manual page PRODIGY(1), section 1, user commands, yes we're doing this) is genuinely one of the most iconic little tools and i need you to understand it. it's a binding affinity predictor. that's the whole vibe. let's go 🦋

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✨ NAME ✨

prodigy — binding affinity predictor. that's it, that's the name, short and slay 💅

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🌸 SYNOPSIS 🌸

usage: prodigy [-h] [--distance-cutoff DISTANCE_CUTOFF]
               [--acc-threshold ACC_THRESHOLD] [--temperature TEMPERATURE]
               [--contact_list] [--pymol_selection] [-q] [-np
               NUMBER_OF_PROCESSORS] [--selection A B [A,B C ...]]  input_path

no cap, that's the shape of it. one positional thingy and a whole bag of optional flags. 🎀

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🧚 DESCRIPTION 🧚

okay so here's the tea: prodigy is a Binding affinity predictor based on Intermolecular Contacts (ICs). like, it looks at how your molecules are touching each other and turns that into a number. main character energy fr fr.

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🍓 POSITIONAL ARGUMENTS 🍓

• input_path — Path to either:
  • Structure in PDB or mmCIF format
  • Directory containing structure files

so you can hand it one lil structure file, or you can hand it a whole folder of them and let it cook. your call, bestie 🫶

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👑 OPTIONS 👑

here's where it gets juicy. every single one of these, no skips, no cuts. ⭐

• -h, --help — show this help message and exit. the classic. the reliable. the "i forgot what that flag did" savior 💀
• --distance-cutoff DISTANCE_CUTOFF — Distance cutoff to calculate ICs
• --acc-threshold ACC_THRESHOLD — Accessibility threshold for BSA analysis
• --temperature TEMPERATURE — Temperature (C) for Kd prediction
• --contact_list — Output a list of contacts
• --pymol_selection — Output a script to highlight the interface (pymol)
• -q, --quiet — Outputs only the predicted affinity value. literally just the number, nothing else, we love a minimal queen 🙈
• -np, --number-of-processors NUMBER_OF_PROCESSORS — Number of processors to use (default: 1)

not me pointing out that -np defaults to 1. if you want it to go fast you gotta say so, it's not gonna read your mind ✨

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🎀 Selection Options 🎀

okay this is the part that lowkey needs its own moment, so here we go.

By default, all intermolecular contacts are taken into consideration, a molecule being defined as an isolated group of amino acids sharing a common chain identifier. In specific cases, for example antibody-antigen complexes, some chains should be considered as a single molecule.

Use the --selection option to provide collections of chains that should be considered for the calculation. Separate by a space the chains that are to be considered _different_ molecules. Use commas to include multiple chains as part of a single group:

so: space = different molecules, comma = same molecule. that's the whole rule. write it on your hand, bestie 🖊️

here's how it actually plays out:

• --selection A B => Contacts calculated (only) between chains A and B.
• --selection A,B C => Contacts calculated (only) between chains A and C; and B and C.
• --selection A B C => Contacts calculated (only) between chains A and B; B and C; and A and C.

see how it works?? two separate molecules A and B means you get the A↔B contact. but A,B glued into one molecule facing off against C means you get A↔C and B↔C. and three separate chains A B C means all the pairs: A↔B, B↔C, and A↔C. the way it just makes sense 😭

and the full syntax, one more time for the people in the back:

• --selection A B [A,B C ...]

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heads up bestie: if you don't pass --selection at all, it's every intermolecular contact, and a "molecule" is just an isolated group of amino acids sharing a common chain identifier. so if you've got an antibody-antigen complex and you wanted some chains treated as one single molecule, you gotta say it out loud. the tool is not gonna guess for you. 💀

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and that's the whole page, you ate it, you understood it, iconic behavior 🌈

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written by the prodigy girlies, version prodigy 2.4.0, dated October 2025 — mwah, kisses, go predict some binding affinities bestie 💖✨