NOMAD-Ref -- visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
What you can do:
Conduct normal mode calculation, even for large proteins and including all atoms, and algorithms that use normal modes for structural refinement or optimization.
Highlights:
- The NOMAD-Ref web server provides tools for online calculation of the normal modes of large molecules (up to 100 000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures.
- Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions.
Keywords:
- macromolecules normal modes calculation tool
- macromolecule motion analysis
- macromolecule dynamics analysis
- macromolecular structure deformation
- protein structure deformation
Literature & Tutorials:
This record last updated: 07-17-2006