Building molecules with YASARA

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:

Build small molecules in seconds using an advanced interactive builder with over 50 functional groups to choose from.
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:

Figure 1: Building amino acids and nucleotides

Figure 2: Building peptides and nucleic acids (clockwise): alpha helix, single unpaired beta strand, left-handed alpha helix, RNA, DNA, 3-10 helix