Linear regression analysis found that either contact order (CO) or long-range order (LRO) parameter has a significant correlation with the logarithms of folding rates. This suggests that sequence separation per contact and total number of contacts are both important in determining the rate of folding. Here, the two factors are incorporated into a new parameter, total contact distance (TCD). Significant improvement in correlation is observed.[See publication #54]

[See publication #65]

Helices in membrane spanning regions are more tightly packed than the helices in soluble proteins. Thus, we introduce a method that uses a simple scale of burial propensity to predict transmembrane helical (TMH) segments. The method correctly predicted the topology of 55 out of 73 proteins (or, 75%) with known three-dimensional structures (the 3D_helix database). This is the best that can be achieved by any current state-of-art methods. [See publication #56]

One of the bottlenecks for the solution of the protein folding problem is the lack of an accurate potential to describe the water-mediated interactions among amino acid residues. Here, we establish a new reference state based on the principle of statistical mechanics. Results show that the new method captures the common water-mediated interactions masked under different compositions of amino acids in the surface, core, and binding interface. [See publication #52]

• Scoring Protein structures or decoys
  
• Predicting mutation-induced change in stability
• Protein-protein binding affinity and discrimination [See publication #61]
• Protein Loop optimazation and selection [See publication #62]