| Name | Description | Type | Package | Framework |
| Component | contains information about a certain Component. | Class | org.biojava.nbio.protmod | BioJava |
| ComponentXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| ModificationCategory | enum ModificationCategorydefine modification categories. | Class | org.biojava.nbio.protmod | BioJava |
| ModificationCondition | Conditions of a protein modification, e. | Interface | org.biojava.nbio.protmod | BioJava |
| ModificationConditionImpl | Class | org.biojava.nbio.protmod | BioJava | |
| ModificationLinkage | Class | org.biojava.nbio.protmod | BioJava | |
| ModificationOccurrenceType | enum ModificationOccurrenceTypeSince:3. | Class | org.biojava.nbio.protmod | BioJava |
| ModifiedCompound | Root interface for all modifications in structure. | Interface | org.biojava.nbio.protmod.structure | BioJava |
| ModifiedCompoundImpl | Class | org.biojava.nbio.protmod.structure | BioJava | |
| ModifiedCompoundXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| ProteinModification | This interface defines information about a specific proteinSince:3. | Interface | org.biojava.nbio.protmod | BioJava |
| ProteinModificationIdentifier | Identify attachment modification in a 3-D structure. | Class | org.biojava.nbio.protmod.structure | BioJava |
| ProteinModificationImpl | This class contains information about a specific proteinSince:3. | Class | org.biojava.nbio.protmod | BioJava |
| ProteinModificationImpl .Builder | Uses Builder pattern to build a ProteinModification. | Class | org.biojava.nbio.protmod | BioJava |
| ProteinModificationRegistry | This class serves as a instance registry by maintaining a pool of ProteinModification instances. | Class | org.biojava.nbio.protmod | BioJava |
| ProteinModificationXmlReader | Class | org.biojava.nbio.protmod.io | 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 | |
| StructureAtomXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| StructureGroup | Information of a group (residue or ligand) involved in a modification. | Class | org.biojava.nbio.protmod.structure | BioJava |
| StructureGroupXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| StructureUtil | Class | org.biojava.nbio.protmod.structure | BioJava | |