9. Resources for reconstructing modified DNA, RNA, and proteinsΒΆ
The following are valuable resources for reconstructing DNA, RNA, and protein modifications:
DNA
RNA
- Modomics: Databases of modified NMPs and modified RNA
- RMBase: Database of posttranscriptionally modified RNAs
- RNA Modification Database: Database of posttranscriptionally modified RNA nucleosides
Proteins
- dbPTM: Database of modified amino acids and proteins
- Delta Mass: Database of modified amino acids
- FindMod: Database of post-translational modifications
- iPTMnet: Database of post-translational modifications
- PDB Chemical Components: Database of modified amino acids
- PDB in Europe Chemical Components: Database of modified amino acids
- Protein Ontology: Database of modified proteins
- PSIMOD: Ontology of modified amino acids
- RESID: Database of modified protein residues
- UniMod: Database of modified amino acids
- UniProt: Database of modified amino acids in proteins
- UniProt Controlled Vocabulary of Posttranslational Modifications: Database of modified amino acids
Drawing structures of monomeric forms
- ChemAxon Marvin: Software for drawing structures of monomeric forms
- Open Babel: Software for calculating the numbers of the atoms in monomeric forms