Ascalaph DNA
Ascalaph DNA is the program for creating models of nucleic acids and their complexes with low-molecular-weight and protein ligands.
Ascalaph DNA has a feature to design a B-DNA model from specially prepared building blocks. Chain Builder contains B-DNA ligands directory with structures of several ligands that can bind to the DNA minor grove. Chain Builder can be extended by adding to it user-created building blocks. The quantum-chemical part of the program can be of great help in building the correct ligand model owing to the possibility of evaluating potential derived partial charges on the atoms and energy barriers for torsion.
The rough model created in the Chain Builder can be refined by means of molecular dynamics. Preliminary refinement can be achieved by simulation in vacuum at low temperature. We recommend calculation at 50-100 K over several hundred picoseconds. It is not recommended to carry out simulation at normal temperature because calculations in vacuum are very rough. In this case, molecular dynamics is used only as a method of optimizing the conformation to get a reasonable preliminary model.
The model optimized in vacuum can further be used for rapid primary assessment, or as a starting model for more comprehensive simulation in explicit solvent. Real molecular dynamics simulations can be performed in dedicated molecular dynamics packages such as MDynaMix/MGE or Ascalaph Liquid.
