Welcome to HyperImmunISE’s documentation!¶
HyperImmunISE is a Python package for generating hyperglycosylated immunogens.
Note
This project is under development.
Contents¶
- Usage
- How Cluster Optimization Works
- Functions
- surface_residues(pdb, min_SASA)
- residue_info(surface_residues, pdb, destination)
- consecutive_residues(resMap)
- consensus_sequences_similarAA()
- identify_native_site(target, query, res_Dict)
- id_double_mutation_similarAA(target, query, query_nat, res_Dict)
- dist(a, b)
- distance_n_atoms(cords)
- allSASD(reslist, jwalk_pdbfile, Jwalk_path, jwalk_map)
- calc_overlap(sphere_rad, distances, priority_sites)
- reduce_clusters(sphere_rad, distances, combinations, priority_sites)
- write_fasta(pdb, destination)
- mutate_fasta(res_to_mutate, allRes, map_dict, mutant_sites, original_fasta, destination)
- run_netNglyc_all(fasta, map_dict, threshold = 6, netnglyc_loc)
- run_netNglyc_chain(fasta, map_dict, threshold = 6,netnglyc_loc)
- coverage_rank(distance_n_atoms, clusters, i, radius = 17.5)
- iterate_clusters(distance_n_atoms, clusters, siteDistances, priority_sites, i, j, initial_r)
- refine_clusters(cluster_list, max_len=0)
- add_glycans(pdb, combo_list, glycan, native_sites, destination, model_glycans)
- Troubleshooting and FAQs
- I am getting an “open: can’t stat file” error
- I am not seeing the scores of the designed constructs
- Are there restrictions on the use of the software?
- Does HyperImmunISE support multi-chain analysis?
- Why should I model glycans using pyRosetta?
- Can I select what types of glycans are added to my designs?
- Why does glycan modelling fail with “Unrecognized sugar 3-letter code ‘fuc’”?
- What value should I select for defining the desired number of glycans?
- There is not a PDB structure available for my target, can I still use this program?
- Can I run HyperImmunISE locally?
- Can I run Amber simulations without a GPU?
- Why can
Output_0.pdbor the selected glycosylation-site combination change between runs?