YASARA provides extensive molecular building facilities:
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
Build atoms and entire amino acid and nucleotide residues (Figure 1).
Figure 1: Building amino acids and nucleotides
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).
Figure 2: Building peptides and nucleic acids (clockwise): alpha helix, single unpaired beta strand, left-handed alpha helix, RNA, DNA, 3-10 helix
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.