9. Resources for reconstructing modified DNA, RNA, and proteins

The following are valuable resources for reconstructing DNA, RNA, and protein modifications:

• DNA

  • DNAmod: Database of covalently modified nuceleobases

  • MethDB: Database of DNA methylation

  • MethSMRT: Database for DNA 6mA and 4mC methylomes

• 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