Examples¶

BPTI Series (Examples 1–4)¶

All four examples build from the same source structure (PDB 6pti, bovine pancreatic trypsin inhibitor), demonstrating progressively more complex modifications to a standard fetch-psfgen-solvate-equilibrate workflow.

Example 1 — baseline solvated build; the simplest complete pestifer workflow
Example 2 — heteroatom exclusion (phosphate ion); salty solvent; retaining crystal waters; validate task with custom parameters
Example 3 — point mutations (two shortcode formats) and disulfide bond deletion
Example 4 — introducing a new disulfide bond via mutations

Small Proteins (Examples 5–6)¶

Straightforward builds of small, single-chain or homodimeric proteins, illustrating ligand inclusion and the reversal of engineered mutations.

Example 5 — HIV-1 protease dimer (1f7a); including small-molecule acetate ligands; reversing engineered mutations
Example 6 — fasciculin 1 from green mamba snake venom (1fas); automatic ionization state assignment via pdb2pqr

HIV-1 Env Ectodomains (Examples 7–12)¶

A family of HIV-1 Env SOSIP trimer builds drawn from several crystal and cryo-EM structures, collectively demonstrating glycan chain management, Fab and ligand exclusion, missing-loop modeling, zero-occupancy terminus handling, user-parameterized small molecules, and stub substitutions for absent loops.

Example 7 — BG505 SOSIP 4zmj; glycan chainID reassignment; missing loop modeling; reversing SOSIP mutations
Example 8 — BG505 4tvp with liganded Fabs removed; multi-chain exclusion of Fab chains, waters, and ions
Example 9 — 8fad; including a user-parameterized small molecule (CGenFF drug fragment)
Example 10 — 8fae; same CGenFF-parameterized drug molecule, different structure
Example 11 — 7txd; loop substitutions; zero-occupancy C-terminus handling; Fab and sCD4 exclusion
Example 12 — 5vn3; Gly₃ stub substitutions for missing V1/V2 loops; sCD4 and Fab exclusion

Insulin Systems (Examples 13–14)¶

Builds involving insulin and its receptor, illustrating homo-oligomeric assembly from an asymmetric unit and Fab exclusion from a large multi-chain complex.

Example 13 — hexameric insulin (2ins); homo-oligomeric assembly from the asymmetric unit
Example 14 — insulin receptor ectodomain (4zxb); large multi-chain complex with bound Fabs removed

SARS-CoV-2 Spike (Example 15)¶

A fully glycosylated BA.2 SARS-CoV-2 spike trimer build, demonstrating glycan grafting from donor structures, missing-loop modeling, and furin cleavage-site handling.

Example 15 — BA.2 spike 7xix; N-glycan grafting from three donor PDB structures; loop modeling; furin cleavage

Membrane-Embedded Systems (Examples 16–17)¶

Both examples embed the same HIV-1 gp41 MPER-TM trimer (6e8w) in a lipid bilayer, contrasting a simple single-lipid membrane with a multi-component viral-mimetic bilayer.

Example 16 — gp41 MPER-TM trimer embedded in a pure DMPC bilayer
Example 17 — same trimer embedded in a multi-lipid viral-mimetic bilayer

Diverse Applications (Examples 18–22)¶

A collection of builds that highlight additional pestifer capabilities: AlphaFold models as input, cofactor-containing enzymes, DNA-protein complexes, and very large multi-chain assemblies.

Example 18 — E. coli replicative DNA polymerase (5fkw); DNA-protein complex with multiple chains and missing loops
Example 19 — sperm whale myoglobin (1mob); heme cofactor handled via standard CHARMM parameters
Example 20 — mitochondrial methylmalonyl-CoA mutase; AlphaFold model (UniProt P22033) as the input source
Example 21 — asymmetric GroEL/GroES chaperonin complex (1aon); 21-chain assembly with ADP ligands
Example 22 — ferredoxin-NADP(H) reductase (2bgj); FAD cofactor; chain exclusion