Useful Constants

The following are potentially useful compile-time constants that maybe of help for writing Lemon workflows. They are all availible in the C++ namespace lemon and the Python module lemon.

const ResidueNameSet lemon::common_peptides{{"CSD"}, {"PCA"}, {"DLE"}, {"KCX"}, {"CAS"}, {"CSO"}, {"PTR"}, {"CME"}, {"SAH"}, {"TPO"}, {"SEP"}, {"MLY"}, {"HYP"}, {"MSE"}, {"CYS"}, {"TRP"}, {"MET"}, {"HIS"}, {"TYR"}, {"GLN"}, {"PHE"}, {"ASN"}, {"PRO"}, {"ARG"}, {"THR"}, {"ASP"}, {"ILE"}, {"LYS"}, {"SER"}, {"GLU"}, {"VAL"}, {"GLY"}, {"ALA"}, {"LEU"},}

Common peptides in the PDB

Names of the most common peptides found in the PDB. This list includes the twenty natural amino acids as well as common post-translation modifications. These were Identified using the ‘peptide_residues’ Lemon workflow.

‘Non-natural’ amino acids:

  • CSD: 3-sulfinoalanine

  • PCA: pyroglutamic acid

  • DLE: D-leucine

  • KCX: lysine nz-carboxylic acid

  • CAS: S-(dimethylarsenic) cysteine

  • CSO: S-hydroxycysteine

  • PTR: O-phosphotyrosine

  • TPO: phosphothreonine

  • SEP: phosphoserine

  • CME: S,S-(2-hydroxyethyl)thiocysteine

  • SAH: S-adenosyl-l-homocysteine

  • MLY: N-dimethyl-lysine

  • HYP: 4-hydroxyproline

  • MSE: selenomethionine

const ResidueNameSet lemon::common_cofactors{{"FAD"}, {"FMN"}, {"NAD"}, {"NAP"}, {"CLA"}, {"HEM"}, {"HEA"}, {"HEB"}, {"HEC"}, {"ADP"}, {"ATP"}, {"GDP"}, {"GTP"}, {"UNL"}, {"CIT"}, {"FLC"}, {"BE7"}, {"MHA"}, {"DHD"}, {"B3P"}, {"BTB"}, {"NHE"}, {"GOL"}, {"DTP"}, {"SAM"}, {"SIA"}, {"ICT"}, {"EPE"}, {"MES"},}

Common co-factors in the PDB

Many proteins require a cofactor to function properly. These cofators are present with the corresponding protein. Common cofactors include: flavin groups (FAD, FMN), nicotinamide groups (NAD, NAP), heme groups ( HEM, HEA, HEB, HEC), nucleotides (ADP, ATP, GDP, GTP), citric acid (CIT, FLC), and S-adenosylmethionine (SAM).

const ResidueNameSet lemon::common_fatty_acids{{"PG6"}, {"PE7"}, {"PG5"}, {"PEU"}, {"PGE"}, {"PIG"}, {"PE8"}, {"PE4"}, {"P33"}, {"C8E"}, {"OTE"}, {"XPE"}, {"N8E"}, {"DR6"}, {"PEG"}, {"2PE"}, {"P6G"}, {"1PE"}, {"SPM"}, {"SPK"}, {"SPD"}, {"1PG"}, {"PG4"}, {"MYR"}, {"OLA"}, {"OLB"}, {"OLC"}, {"PLM"}, {"PEE"}, {"LHG"}, {"MC3"}, {"PAM"},}

Common fatty-acids in the PDB

Several protein crystal structures contain fatty acids used to help induce crystallization. This list contains fatty acids and other ‘linear’ small molecules.

const std::unordered_set<std::string> lemon::small_molecule_types{{"NON-POLYMER"}, {"OTHER"}, {"PEPTIDE-LIKE"}}

Linkage types for small-molecules in the PDB

This set contains the types of linkages used to initially identify a small molecule in a crystal structure.*PEPTIDE-LIKE* is included here becasue many drugs are classified with this linkage.

Note: the following constant is not availible in Python as it is meant for launching Lemon, not for use in workflows.

const std::unordered_set<std::string> lemon::large_entries{{"3J3Q"}, {"3J3Y"}, {"5Y6P"}}

PDB entries that should be skipped as they are time consuming to calculate.

These PDB entries are of virus capsids and therefore are time consuming to perform operations on. The typical user may wish to skip these entries as to reduce the total amount of time required for a Lemon workflow. These entries are indentified as they take an order of magnitude longer to perform an operation than other entries.