Gouthaman S. Balaraman

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We present a critical assessment of the performance of our homology model refinement method for G protein-coupled receptors (GPCRs), called LITICon that led to top ranking structures in a recent structure prediction assessment GPCRDOCK2010. GPCRs form the largest class of drug targets for which only a few crystal structures are currently available.(More)
After a traumatic event, people often report using alcohol to relieve their symptoms of anxiety, irritability, and depression. Alcohol may relieve these symptoms because drinking compensates for deficiencies in endorphin activity following a traumatic experience. Within minutes of exposure to a traumatic event there is an increase in the level of endorphins(More)
Recent experiments to derive a thermally stable mutant of turkey beta-1-adrenergic receptor (beta1AR) have shown that a combination of six single point mutations resulted in a 20 degrees C increase in thermal stability in mutant beta1AR. Here we have used the all-atom force-field energy function to calculate a stability score to detect stabilizing point(More)
Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be(More)
The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward "native-like" structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement.(More)
Classical molecular dynamics simulations are performed to cover Stark mixing transitions (n → n ′) in Rydberg atoms by collision with slow ions. Accuracy is tested by comparison with the exact analytical classical probabilities P ′ previously obtained when the ion–atom potential is taken as the long-range ion–dipole interaction. The results are provided not(More)
An efficient geometric integrator is proposed for solving the perturbed Kepler motion. This method is stable and accurate over long integration time, which makes it appropriate for treating problems in astrophysics, like solar system simulations, and atomic and molecular physics, like classical simulations of highly excited atoms in external fields. The key(More)
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