Novel Computational Tool for Understanding Protein Interactions and Generating Energy Maps

Generation of the interior and exterior residues, which are predominantly hot and cold, respectively (red/salmon = high, white = middle, cyan/blue = low μ-factors), in a catalytic site of an enzyme using the novel computational model.

Invention Summary:

Most computational models rely on large numbers of weak interactions to describe protein energetics. One challenge of folding a protein through computer modeling and simulations using quantum mechanics lies in finding the global minimum of the protein conformational energy landscape which corresponds to a region close to the global energy minimum. There is therefore a need for improved and/or complementary analysis tools for understanding, predicting, and designing protein and/or peptide behavior, intra- and inter- protein interactions, and the three-dimensional structure of proteins based on the primary amino acid sequence.

Rutgers researcher Dr. Lawrence Williams has developed a computer-implemented method and system for modeling the three-dimensional structure of a protein by generating an energy map for peptides and/or proteins given the amino acid sequence and a per-residue conformation index.  The description of proteins in terms of per-residue interaction potentials allows proteins to be understood both qualitatively and quantitatively. CHARMM, a top performing force-field simulation software package, and Watermap, the most widely accepted best-performing solvation computational tool, both require long computing times (hours or days), while the novel proposed method performs in much shorter periods (seconds).


A computational tool which can be utilized for designing drugs, protein mutation studies, 3D protein folding, and protein engineering.



  • Superior performance as compared to existing computational methods (seconds vs hours/days).
  • Better quantitative and qualitative understanding of proteins.

Intellectual Property & Development Status

Patent Pending. Software available. Intellectual property available for licensing and/or research collaboration.

Patent Information:
For Information, Contact:
Dan Benderly
Licensing Manager
Rutgers University