Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge. - Gerhard König; Frank C. Pickard IV; Jing Huang 004; Andrew C. Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O. Dral; Samarjeet Prasad; Michael R. Jones; Yihan Shao; Walter Thiel; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2016)

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. - Samarjeet Prasad; Jing Huang 004; Qiao Zeng; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

A deep learning approach for the blind logP prediction in SAMPL6 challenge. - Samarjeet Prasad; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2020)

Variational embedding of protein folding simulations using gaussian mixture variational autoencoders. - Mahdi Ghorbani; Samarjeet Prasad; Jeffery B. Klauda; Bernard R. Brooks (CoRR, 2021)

The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. - Samarjeet Prasad; Andrew C. Simmonett; Rubén Meana-Pañeda; Bernard R. Brooks (J. Comput. Chem., 2021)

GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules. - Mahdi Ghorbani; Samarjeet Prasad; Jeffery B. Klauda; Bernard R. Brooks (CoRR, 2022)

Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. - Phillip S. Hudson; Félix Aviat; Rubén Meana-Pañeda; Luke C. Warrensford; Benjamin C. Pollard; Samarjeet Prasad; Michael R. Jones; H. Lee Woodcock III; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2022)