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Building molecules with YASARA

YASARA provides extensive molecular building facilities:

Ras effector Nore1
Figure 1: Building amino acids and nucleotides
Knowledge-based potentials
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).
  • Ras effector Nore1
    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).
  • Knowledge-based potentials
    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.
Additional features in YASARA Model and above:
Additional features in YASARA Dynamics and above:



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