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The Dark Proteome & Pathological Models

This directory contains examples of "Dark Proteome" proteins—intrinsically disordered regions (IDRs), orphans, and highly flexible ensembles—as well as a collection of "Pathological Models" designed to test the limits of structural biology software, visualization tools, and physics engines.

Warning: Pathological Geometry

The models in the "Hall of Pathological Perversions" are intentionally designed to violate physical and geometric constraints. They may cause some structural biology software to crash or behave unexpectedly.

💀 The Hall of Pathological Perversions

The following models represent intentional violations of biophysical laws, geometric constraints, and chemical sanity:

  1. mobius_loop_pathological.pdb: A cyclic peptide generated with high internal strain to simulate a Moebius-like topology, forcing the backbone into a self-intersecting circular path.
  2. trp_singularity.pdb: A 20-residue poly-tryptophan chain built with zero clash refinement. It features a physically impossible density of aromatic rings packed into the same space.
  3. mirror_nightmare.pdb: The "Anti-Protein." Composed entirely of D-amino acids, it represents a complete chiral inversion of a standard peptide, creating a "mirror image" world of structural biology.
  4. chiral_chimera.pdb: A sequence of alternating L and D amino acids. This destroys the standard regularity of the protein backbone, making it impossible to form stable helices or sheets.
  5. amyloid_nightmare.pdb: A multi-chain stack of beta-sheets where the inter-chain distances have been reduced to values that would lead to immediate atomic fusion in a real system.
  6. steric_singularity.pdb: A 50-residue chain pathologically compressed into a 5Å sphere. It violates every known Van der Waals radius and creates a coordinate density "black hole."
  7. fractal_spaghetti.pdb: A 200-residue random walk that uses discontinuous fractal-like coordinates, causing the chain to "teleport" across space every 10 residues.
  8. entropic_abyss_ensemble.pdb: A 10-model ensemble where each model is a completely different, maximally high-entropy random state for the same sequence, representing total conformational chaos.
  9. infinity_coil.pdb: A 100-residue minimized chain featuring alternating regions of alpha-helix and beta-sheet, pushed to the limits of sequence-structure compatibility.
  10. flatland_protein.pdb: The "2D Protein." Every Z-coordinate has been zeroed out, forcibly collapsing a 3D folded structure into a perfectly flat, impossible 2-dimensional plane with massive overlaps.
  11. proline_alpha_helix.pdb: A poly-proline chain hard-coded into an ideal alpha-helical conformation. Because proline sidechains are rigid rings that lack amide hydrogens for H-bonding, this creates catastrophic, unfixable steric clashes.
  12. exploded_protein.pdb: The "Macro-Protein." All inter-atomic distances have been scaled up by exactly 10x, creating a structure that looks like a protein but possesses giant, 15-Angstrom "covalent" bonds.
  13. eclipsed_chain.pdb: The "Ramachandran Violation." Every single \(\phi\) and \(\psi\) dihedral angle is forced to exactly \(0.0^\circ\), creating a maximally eclipsed geometry that represents a global peak of steric repulsion.
  14. z_fighting_chimera.pdb: The "Z-Fighting Nightmare." A two-chain complex where Chain A (poly-Alanine) and Chain B (poly-Tryptophan) share the exact same spatial coordinates, resulting in an impossible molecular superposition.
  15. black_hole_protein.pdb: The "Black Hole Protein." A 50-residue sequence where every single atomic coordinate is exactly (0.000, 0.000, 0.000), simulating a total spatial collapse.
  16. spaghetti_knot.pdb: The "Spaghetti Knot." A 20-chain complex where every single chain is independently generated and then centered at the exact origin, causing all 20 chains to inextricably overlap in a tangled mass.
  17. overflow_protein.pdb: The "Coordinate Overflow." Coordinates are forced past the 9999.999 limit (9999999.9), intentionally breaking the strict PDB 8.3f fixed-width column format to crash legacy parsers.
  18. antimatter_protein.pdb: The "Antimatter Protein." All atomic occupancies are set to -1.00 and all B-factors to -99.99, breaking standard biophysical assumptions about disorder and probabilities.
  19. schrodingers_residue.pdb: "Schrodinger's Residue." Two overlapping altloc records (A and B) share the exact same spatial coordinates, but record A is Carbon and record B is Uranium. A true structural superposition.

🧬 Biological Dark Proteome Examples

These models represent real-world biological complexity found in disordered or non-standard systems:

  • alpha_syn_demo.pdb: A model of Alpha-synuclein, a classic intrinsically disordered protein (IDP) involved in Parkinson's disease.
  • tdp43_disordered.pdb: The low-complexity domain of TDP-43, known for its role in liquid-liquid phase separation (LLPS) and ALS.
  • ubiquitin_standard_candle.pdb: A high-resolution reference model used as a "standard candle" for NMR and Cryo-EM validation.
  • apela_orphan.pdb: A model of the Apela peptide, an "orphan" ligand with high conformational flexibility.
  • xcl1_hallucination_alpha.pdb / xcl1_hallucination_beta.pdb: Metamorphic protein states (XCL1) that can switch between entirely different folds.
  • ybea_knot_attempt.pdb: An exploration of knotted protein topologies.

🛠️ Scripts & Tools

  • cryo_em_demo.py: Script to generate synthetic Cryo-EM maps from these ensembles.
  • ensemble_demo.py: Demonstrates how to load and analyze multi-model ensembles in synth-pdb.