# Template Catalog
This catalog lists all residue templates available in BioForge, with their usage and pH ranges for protonation states.
## Protein Templates
These templates cover all standard amino acids plus their titration-dependent labels. Alternate names (ASH, GLH, LYN, etc.) describe the protonation state that the hydrogenation pass will swap in at the given pH.
| **"ALA"** | `ALA` | 0 | (−∞, +∞) | Alanine with a compact methyl side chain used as a neutral hydrophobic scaffold. |
| **"ARG"** | `ARG` | +1 | (−∞, 12.5] | Arginine in its guanidinium cation form; dominant across physiological pH. |
| **"ARN"** | `ARG` | 0 | (12.5, +∞) | Neutral arginine reached after guanidinium deprotonation at very high pH. |
| **"ASN"** | `ASN` | 0 | (−∞, +∞) | Asparagine with a polar carboxamide side chain. |
| **"ASP"** | `ASP` | −1 | [3.9, +∞) | Aspartate with a deprotonated carboxylate group. |
| **"ASH"** | `ASP` | 0 | (−∞, 3.9) | Aspartic acid with a protonated carboxyl, favored in strongly acidic media. |
| **"CYS"** | `CYS` | 0 | (−∞, 8.3] | Cysteine with a neutral thiol, used below the thiol pKₐ. |
| **"CYM"** | `CYS` | −1 | (8.3, +∞) | Cysteine thiolate after sulfur deprotonation. |
| **"CYX"** | `CYS` | 0 | (−∞, +∞) | Disulfide-bonded cystine label assigned whenever SG–SG distance indicates a bridge. |
| **"GLN"** | `GLN` | 0 | (−∞, +∞) | Glutamine with a polar carboxamide side chain. |
| **"GLU"** | `GLU` | −1 | [4.2, +∞) | Glutamate with a deprotonated γ-carboxylate. |
| **"GLH"** | `GLU` | 0 | (−∞, 4.2) | Glutamic acid with a protonated γ-carboxyl. |
| **"GLY"** | `GLY` | 0 | (−∞, +∞) | Glycine, the smallest amino acid lacking a side chain carbon. |
| **"HID"** | `HIS` | 0 | [6.0, +∞) | Neutral histidine tautomer protonated on ND1 (δ) as selected by the configured strategy. |
| **"HIE"** | `HIS` | 0 | [6.0, +∞) | Neutral histidine tautomer protonated on NE2 (ε) as selected by the configured strategy. |
| **"HIP"** | `HIS` | +1 | (−∞, 6.0) | Histidine imidazolium carrying two protons in acidic conditions. |
| **"ILE"** | `ILE` | 0 | (−∞, +∞) | Isoleucine with a β-branched hydrophobic side chain. |
| **"LEU"** | `LEU` | 0 | (−∞, +∞) | Leucine with a γ-branched hydrophobic side chain. |
| **"LYS"** | `LYS` | +1 | (−∞, 10.5] | Lysine with a protonated ε-ammonium group. |
| **"LYN"** | `LYS` | 0 | (10.5, +∞) | Neutral lysine formed after ε-amino deprotonation at very high pH. |
| **"MET"** | `MET` | 0 | (−∞, +∞) | Methionine featuring a thioether side chain. |
| **"PHE"** | `PHE` | 0 | (−∞, +∞) | Phenylalanine with an aromatic phenyl ring. |
| **"PRO"** | `PRO` | 0 | (−∞, +∞) | Proline with a pyrrolidine ring that constrains backbone φ. |
| **"SER"** | `SER` | 0 | (−∞, +∞) | Serine with a hydroxymethyl side chain. |
| **"THR"** | `THR` | 0 | (−∞, +∞) | Threonine with a β-branched hydroxyethyl group. |
| **"TRP"** | `TRP` | 0 | (−∞, +∞) | Tryptophan bearing an indole aromatic system. |
| **"TYR"** | `TYR` | 0 | (−∞, 10.0] | Tyrosine with an intact phenolic OH. |
| **"TYM"** | `TYR` | −1 | (10.0, +∞) | Tyrosinate, the phenolate form of tyrosine favored under strongly basic conditions. |
| **"VAL"** | `VAL` | 0 | (−∞, +∞) | Valine with a branched hydrophobic isopropyl side chain. |
_Neutral histidines (`HID` / `HIE`) share the same pH interval; BioForge chooses between them using `HydroConfig.his_strategy` (default: hydrogen-bond network analysis)._
## Nucleic Acid Templates
RNA entries use ribose sugars (A, C, G, U, I) while DNA entries carry the `D` prefix. All nucleotides carry a −1 charge from the phosphate and remain valid at any pH because the hydrogenation pass does not titrate nucleic acids.
| **"A"** | `A` | −1 | (−∞, +∞) | RNA adenosine residue with adenine base and 2′-hydroxyl ribose. |
| **"C"** | `C` | −1 | (−∞, +∞) | RNA cytidine residue carrying cytosine and ribose. |
| **"G"** | `G` | −1 | (−∞, +∞) | RNA guanosine residue with guanine and ribose. |
| **"U"** | `U` | −1 | (−∞, +∞) | RNA uridine residue with uracil and ribose. |
| **"I"** | `I` | −1 | (−∞, +∞) | RNA inosine residue (hypoxanthine base) commonly used in tRNA. |
| **"DA"** | `DA` | −1 | (−∞, +∞) | DNA deoxyadenosine residue lacking the ribose 2′-hydroxyl. |
| **"DC"** | `DC` | −1 | (−∞, +∞) | DNA deoxycytidine residue. |
| **"DG"** | `DG` | −1 | (−∞, +∞) | DNA deoxyguanosine residue. |
| **"DT"** | `DT` | −1 | (−∞, +∞) | DNA thymidine residue. |
| **"DI"** | `DI` | −1 | (−∞, +∞) | DNA deoxyinosine residue for inosine-containing duplexes. |
## Solvent Templates
| **"HOH"** | `HOH` | 0 | (−∞, +∞) | Water molecule used for explicit solvent records. |