At 11/18/04, H.Iiduka wrote: >1.How to detect monomer-monomer interactions, H-bonds, hydrophobic > interactions and electrostatic interactions etc. And Which visualization- > tool is best for visualizing them? The "best" is a matter of personal preference. A very easy to use, yet powerful tool is Protein Explorer (proteinexplorer.org, which is largely my own work). Noncovalent interactions between any selected moiety and the remainder of the PDB file are displayed in a few clicks at the QuickViews control panel: SELECT (moiety), DISPLAY Contacts (try both options). QuickViews also has one-click displays of cation-pi interactions and salt bridges. >2.Are there any tools to predict quaternary structures and it's interaction > sites from tertiary structures? The Probable Quaternary Structures (PQS) site at EBI is a very good one for crystallographically-determined tertiary structures. You can access it in Protein Explorer: click on "PE Site Map" (near the Zoom button in QuickViews), then External Resources. PQS offers you the coordinates for predicted multimers, with links to display them directly in Protein Explorer. ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz