| YASARA provides extensive molecular building facilities:
- 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 changes.
Additional features in YASARA Model 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 proteins.
Additional features in YASARA Dynamics and above:
- Crystallize proteins to fill the crystallographic unit cell.
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Figure 1: Building amino acids and nucleotides
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Figure 2: Building peptides and nucleic acids
(clockwise): alpha helix, single unpaired beta strand, left-handed alpha helix, RNA,
DNA, 3-10 helix
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