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Examples Gallery

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Basic Structures

Alpha Helix

The most common secondary structure in proteins.

Alpha Helix Example

synth-pdb --length 20 --conformation alpha --visualize

Features: - 3.6 residues per turn - 5.4 Å pitch - Hydrogen bonds between i and i+4 residues

Beta Sheet

Extended conformation with characteristic pleated structure.

Beta Sheet Example

synth-pdb --length 20 --conformation beta --visualize

Features: - Extended backbone (phi ≈ -120°, psi ≈ +120°) - 3.3 Å between residues - Parallel or antiparallel arrangements

Random Coil

Disordered structure with diverse conformations.

Random Coil Example

synth-pdb --length 20 --conformation random --visualize

Features: - Ramachandran angles sampled from allowed regions - No regular secondary structure - Useful for testing flexibility

Biologically-Inspired Structures

Leucine Zipper

Classic coiled-coil motif with hydrophobic interface.

Leucine Zipper Example

synth-pdb --sequence "LKELEKELEKELEKELEKELEKEL" \
    --conformation alpha \
    --minimize \
    --visualize

Scientific Context: - Heptad repeat pattern (a-b-c-d-e-f-g) - Leucines at 'a' and 'd' positions form hydrophobic core - Found in transcription factors (e.g., GCN4, c-Fos, c-Jun)

Zinc Finger

DNA-binding motif coordinating Zn²⁺ ion.

Zinc Finger Example

synth-pdb --sequence "CPHCGKSFSQKSDLVKHQRT" \
    --structure "1-10:beta,11-20:alpha" \
    --metal-ions auto \
    --minimize \
    --visualize

Scientific Context: - Cys₂His₂ coordination of Zn²⁺ - Beta-hairpin + alpha-helix architecture - Found in transcription factors (e.g., TFIIIA, Sp1)

Collagen Triple Helix

Unique left-handed helix with Gly-X-Y repeats.

Collagen Example

synth-pdb --sequence "GPPGPPGPPGPPGPPGPPGPP" \
    --conformation polyproline \
    --minimize \
    --visualize

Scientific Context: - Gly-Pro-Pro repeat pattern - Left-handed helix (opposite of alpha helix) - Three chains intertwine to form triple helix

Silk Fibroin

Beta-sheet-rich structure with Ala-Gly repeats.

synth-pdb --sequence "AGAGAGAGAGAGAGAGAGAG" \
    --conformation beta \
    --minimize \
    --visualize

Scientific Context: - Alanine-glycine repeats - Antiparallel beta sheets - High tensile strength

Advanced Features

Cyclic Peptide

Head-to-tail cyclized structure.

synth-pdb --sequence "GGGGGGGGGGGG" \
    --cyclic \
    --minimize \
    --visualize

Applications: - Drug design (improved stability) - Examples: Cyclosporine A, Oxytocin

Disulfide Bonds

Covalent cross-links between cysteine residues.

synth-pdb --sequence "CGGGGGGGGGGC" \
    --conformation alpha \
    --minimize \
    --visualize

Features: - Automatic detection of Cys pairs within 2.0-2.2 Å - Stabilizes protein structure - Common in extracellular proteins

Mixed Secondary Structures

Helix-turn-helix motif.

synth-pdb --sequence "ACDEFGHIKLMNPQRSTVWY" \
    --structure "1-7:alpha,8-13:random,14-20:alpha" \
    --minimize \
    --visualize

Features: - Multiple secondary structure regions - Realistic protein architecture - Useful for testing fold recognition

D-Amino Acids

Mirror-image amino acids for peptide design.

synth-pdb --sequence "ALA-dALA-GLY-dGLY-SER-dSER" \
    --conformation alpha \
    --minimize \
    --visualize

Applications: - Protease resistance - Drug design - Retro-inverso peptides

NMR Data Generation

Chemical Shifts

Generate structure with predicted NMR chemical shifts.

synth-pdb --length 30 \
    --conformation alpha \
    --gen-shifts \
    --output nmr_structure.pdb

Output: NEF file with ¹H, ¹³C, ¹⁵N chemical shifts

Relaxation Rates

Generate structure with NMR relaxation data.

synth-pdb --length 30 \
    --conformation alpha \
    --gen-relax \
    --output nmr_structure.pdb

Output: NEF file with R₁, R₂, NOE values

NOE Restraints

Generate distance restraints for structure calculation.

synth-pdb --length 30 \
    --conformation alpha \
    --gen-nef \
    --output nmr_structure.pdb

Output: NEF file with NOE distance restraints

Dataset Generation

Bulk Generation

Generate 1,000 diverse structures for ML training.

synth-pdb --mode dataset \
    --num-samples 1000 \
    --min-length 10 \
    --max-length 50 \
    --output ./training_data

Output Structure: 

training_data/
├── dataset_manifest.csv
├── train/ (800 structures)
└── test/ (200 structures)

Hard Decoys

Generate challenging negative samples.

synth-pdb --mode decoys \
    --sequence ACDEFGHIKLMNPQRSTVWY \
    --drift 5.0 \
    --num-samples 100 \
    --output ./decoys

Use Cases: - Training robust AI models - Testing structure validation tools - Benchmarking scoring functions

Multimodal Observables

Simulate integrated data from multiple structural biology techniques. For a hands-on demonstration, see the Cryo-EM & SAXS Lab.

Cryo-EM Density Maps

Generate 3D density volumes at a specific resolution.

Cryo-EM Map Example

synth-pdb --mode cryo-em \
    --sequence "MEELQK" \
    --resolution 4.0 \
    --output synthetic_map.mrc

Scientific Context: - Simulates electron density at different resolutions (3.0Å - 10Å). - Essential for testing map-to-model fitting algorithms. - Supports ensemble averaging for flexible proteins.

SAXS Profiles

Simulate Small-Angle X-ray Scattering solution data.

SAXS Profile Example

synth-pdb --mode saxs \
    --sequence "NSDSECPLSHDGYCLHDGVCMYIEALDKY" \
    --q-max 0.4 \
    --output protein_saxs.dat

Scientific Context: - Uses the Debye formula to compute \(I(q)\) vs \(q\). - Probes the global shape and "compactness" of a protein. - Includes solvent subtraction (hydration shell) effects.

Docking Preparation

Convert PDB to PQR for electrostatic and docking software.

synth-pdb --mode docking \
    --sequence "ACDEFGHIK" \
    --output ready_for_docking.pqr

Scientific Context: - Assigns partial charges and Van der Waals radii. - Uses OpenMM and AMBER forcefields for parameterization. - Standard input for APBS and many protein-ligand docking engines.

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