| Name | Description | Type | Package | Framework |
| ModifiedCompound | Root interface for all modifications in structure. | Interface | org.biojava.nbio.protmod.structure | BioJava |
| ModifiedCompoundImpl | Class | org.biojava.nbio.protmod.structure | BioJava | |
| ProteinModificationIdentifier | Identify attachment modification in a 3-D structure. | Class | org.biojava.nbio.protmod.structure | BioJava |
| StructureAtom | Everything that is needed to uniquely describe a atom. | Class | org.biojava.nbio.protmod.structure | BioJava |
| StructureAtomLinkage | Class | org.biojava.nbio.protmod.structure | BioJava | |
| StructureGroup | Information of a group (residue or ligand) involved in a modification. | Class | org.biojava.nbio.protmod.structure | BioJava |
| StructureUtil | Class | org.biojava.nbio.protmod.structure | BioJava | |