YASARA provides extensive molecular
Additional features in YASARA Model and above:
- Build atoms and entire amino acid and nucleotide
residues (Figure 1).
- Add residues to the C-terminal or 3' end, arriving at
peptides and nucleic acids. The backbone dihedral angles can be
specified directly to let the macromolecule adopt a certain
conformation (Figure 2).
- Build stretched-out proteins and nucleic acids
directly from FASTA sequence files.
- Exchange residues to model point mutations.
- Add terminal oxygens to proteins.
- De-novo building of small molecules, make chemical
modifications to existing molecules. Hydrogens adapt automatically to
Additional features in YASARA Dynamics and above:
- Automatically correct problems like missing atoms etc.
- Oligomerize proteins to adopt their biologically
relevant quaternary structure.
- Add terminal acetyl- and N-methyl capping groups to
- Crystallize proteins to fill the crystallographic
|Figure 1: Building amino acids and
|Figure 2: Building peptides and
nucleic acids (clockwise): alpha helix, single unpaired beta strand,
left-handed alpha helix, RNA, DNA, 3-10 helix