.. _examples: Examples ======== .. toctree:: :hidden: :maxdepth: 1 examples/ex01/bpti1 examples/ex02/bpti2 examples/ex03/bpti3 examples/ex04/bpti4 examples/ex05/hiv-protease examples/ex06/green-mamba-toxin examples/ex07/hiv-sosip-env-ectodomain1 examples/ex08/hiv-sosip-env-ectodomain2 examples/ex09/hiv-ad8-env-ectodomain examples/ex10/hiv-ae2-env-ectodomain examples/ex11/hiv-sosip-env-ectodomain3 examples/ex12/hiv-sosip-env-ectodomain4 examples/ex13/insulin-hexamer examples/ex14/insulin-receptor-ectodomain examples/ex15/sars-cov2-S-BA2 examples/ex16/hiv-mpertm3-membrane1 examples/ex17/hiv-mpertm3-membrane2 examples/ex18/ecoli-polymerase examples/ex19/sperm-whale-myoglobin examples/ex20/methylmalonyl-coa-mutase examples/ex21/groel-groes-adp examples/ex22/ferredoxin-fad 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. - :doc:`Example 1 ` — baseline solvated build; the simplest complete pestifer workflow - :doc:`Example 2 ` — heteroatom exclusion (phosphate ion); salty solvent; retaining crystal waters; ``validate`` task with custom parameters - :doc:`Example 3 ` — point mutations (two shortcode formats) and disulfide bond deletion - :doc:`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. - :doc:`Example 5 ` — HIV-1 protease dimer (1f7a); including small-molecule acetate ligands; reversing engineered mutations - :doc:`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. - :doc:`Example 7 ` — BG505 SOSIP 4zmj; glycan chainID reassignment; missing loop modeling; reversing SOSIP mutations - :doc:`Example 8 ` — BG505 4tvp with liganded Fabs removed; multi-chain exclusion of Fab chains, waters, and ions - :doc:`Example 9 ` — 8fad; including a user-parameterized small molecule (CGenFF drug fragment) - :doc:`Example 10 ` — 8fae; same CGenFF-parameterized drug molecule, different structure - :doc:`Example 11 ` — 7txd; loop substitutions; zero-occupancy C-terminus handling; Fab and sCD4 exclusion - :doc:`Example 12 ` — 5vn3; Gly\ :sub:`3` 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. - :doc:`Example 13 ` — hexameric insulin (2ins); homo-oligomeric assembly from the asymmetric unit - :doc:`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. - :doc:`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. - :doc:`Example 16 ` — gp41 MPER-TM trimer embedded in a pure DMPC bilayer - :doc:`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. - :doc:`Example 18 ` — *E. coli* replicative DNA polymerase (5fkw); DNA-protein complex with multiple chains and missing loops - :doc:`Example 19 ` — sperm whale myoglobin (1mob); heme cofactor handled via standard CHARMM parameters - :doc:`Example 20 ` — mitochondrial methylmalonyl-CoA mutase; AlphaFold model (UniProt P22033) as the input source - :doc:`Example 21 ` — asymmetric GroEL/GroES chaperonin complex (1aon); 21-chain assembly with ADP ligands - :doc:`Example 22 ` — ferredoxin-NADP(H) reductase (2bgj); FAD cofactor; chain exclusion