| * | Proposed symbol of phosphate group |
| ~ | Proposed symbol of amidation |
| BLAST | Basic Local Alignment Search Tool |
| BRENDA | Braunschweig Enzyme Database |
| [C@] and [C@@] | Symbols of chiral carbon atoms in SMILES code |
| CID | Compound Identifier (in PubChem database) |
| ΔF | Symbol of dehydrophenylalanine according to the SATPdb database |
| EMBL | European Molecular Biology Laboratory |
| EROP-Moscow | Endogenous Regulatory OligoPeptide knowledgebase-Moscow |
| HELM | Hierarchical Editing Language for Macromolecules |
| Hyl | Hydoxylysine |
| Hyp | Hydroxyproline |
| InChI | International Chemical Identifier |
| InChIKey | Key of International Chemical Identifier |
| IUPAC | International Union of Pure and Applied Chemistry |
| LINUCS | LInear Notation for Unique description of Carbohydrate Sequences |
| NCBI | National Center for Biotechnology Information |
| P | Depending on the context, one-letter symbol of proline or phosphorus symbol |
| p | Depending on context, one-letter symbol of D-proline or symbol of phosphorylation of amino acid residue |
| R | One-letter symbol of arginine |
| (R) | Proposed symbol of configuration of substituents around asymmetric atom: “Rectus” |
| S | One-letter symbol of serine |
| (S) | Proposed symbol of configuration of substituents around asymmetric atom: “Sinister” |
| SATPdb | Structurally Annotated Therapeutic Peptides database |
| SLN | SYBYL Line Notation |
| SMILES | Simplified Molecular Input Line Entry System or Simplified Molecular Input Line Entry Specification |
| UWM | University of Warmia and Mazury in Olsztyn, Poland |