Assessment of methods used for predicting lipophilicity: Application to nucleosides and nucleoside bases. - Vellarkad N. Viswanadhan; M. Rami Reddy; Russell J. Bacquet; Mark D. Erion (J. Comput. Chem., 1993)

Calculation of Relative Free Energy Differrences for the Covalent Hydration of Organic Compounds: A Combined Quantum Mechanical and Free Energy Perturbation Study. - Mark D. Erion; M. Rami Reddy (J. Comput. Chem., 1995)

Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques. - N. Swamy Kandadai; M. Rami Reddy (J. Comput. Chem., 1996)

Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields. - M. Rami Reddy; Mark D. Erion; Atul Agarwal; Vellarkad N. Viswanadhan; D. Quentin McDonald; W. Clark Still (J. Comput. Chem., 1998)

Calculation of relative solvation free energy differences by thermodynamic perturbation method: Dependence of free energy results on simulation length. - M. Rami Reddy; Mark D. Erion (J. Comput. Chem., 1999)

Calculation of relative binding affinities of fructose 1, 6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method. - Ravichandra Mutyala; R. N. Reddy; M. Sumakanth; P. Reddanna; M. Rami Reddy (J. Comput. Chem., 2007)

Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies. - M. Rami Reddy; U. C. Singh; Mark D. Erion (J. Comput. Chem., 2007)

Homology modeling of 5-lipoxygenase and hints for better inhibitor design. - P. Aparoy; R. N. Reddy; Lalitha Guruprasad; M. Rami Reddy; P. Reddanna (J. Comput. Aided Mol. Des., 2008)

Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length. - M. Rami Reddy; Mark D. Erion (J. Comput. Aided Mol. Des., 2009)

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose-1, 6-bisphosphatase inhibitors. - R. S. Rathore; P. Aparoy; P. Reddanna; Anand K. Kondapi; M. Rami Reddy (J. Comput. Chem., 2011)