Algorithms to identify left-handed poly(Pro)II type (P_II) structures in globular proteins were developed ^Abstract . Molecular dynamics simulations on oligopeptides in a-helix, b-strand and P_II conformations were performed to understand the differences in their behaviors influenced by hydration^Abstract.

Predicting the secondary structure of proteins from their CD spectra: The self-consistent method^Abstract (SELCON) for protein CD spectral analysis was developed and used in the prediction of the P_II structure in globular protiens^Abstract . Recently, methods were developed to predict the number of a-helical and b-strand segments in a protein from its CD spectrum^Abstract. The methods were used in the investigation of T7 RNA polymerase structure^{Abstract;Abstract}.
Calculating the CD spectra from structure: The inverse approach of computing the CD spectrum for a given structure, from either model building or x-ray crystallography, has also been examined. The transition parameters were developed and used in the calculation of CD spectra by matrix method. Using these methods  fd gene 5 protein^Abstract, BPTI^Abstract and model oligonucleotide^Abstract CD spectra were calculated. Recently, we have calculated the CD spectra of a set of proteins we used in CD analyses^Abstract.

The fractions of secondary structures and the number of a-helical and b-strand segments in a protein can be predicted from the CD spectrum using the methods we have developed^Abstract. We are working towards utilizing this information in sequence-based protein structure prediction methods.

 Research Experience

Biophysical Chemistry:

• Applying theoretical methods (ab initio quantum chemical and semi-empirical) to study biologically important systems
• Transition moment calculation from semi-empirical methods
• Calculation of circular dichroism spectra of proteins and nucleic acids
• Calculation of aromatic contributions to the protein circular dichroism spectra
• Potential energy calculations (empirical)
• Analysis of protein CD spectra
• Identifying secondary structure of proteins
• Molecular dynamics simulations

• Protein secondary structure analysis from CD spectroscopy
• Experimental and theoretical studies of the CD spectra of proteins
• Predicting a-helical and b-strand segments in proteins from CD spectra.

• Ab initio calculations of model systems of biologically important molecules
• Combining molecular dynamics with CD calculations
• Molecular dynamics simulations of oligopeptides and proteins
• Development of algorithms to identify secondary structure of proteins

• Developed SELCON, computer program to analyze protein CD spectra
• Developed methods to analyze molecular dynamics trajectories
• Developed methods to identify poly(Pro)II structure in proteins
• Experience with major molecular modeling softwares (AMBER, GROMOS, INSIGHT, etc.)
• Experience with neural network methods
• Familiarity with FORTRAN, C++ and PASCAL programming languages.