Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. - F. Marty Ytreberg; Daniel M. Zuckerman (J. Comput. Chem., 2004)

Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data. - Conrad Shyu; F. Marty Ytreberg (J. Comput. Chem., 2009)

Accurate estimation of solvation free energy using polynomial fitting techniques. - Conrad Shyu; F. Marty Ytreberg (J. Comput. Chem., 2011)

Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure. - Kuo-Hao Lee; F. Marty Ytreberg (Entropy, 2012)

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations. - Jagdish Suresh Patel; Celeste J. Brown; F. Marty Ytreberg; Deborah L. Stenkamp (PLoS Comput. Biol., 2018)

Implementation of adaptive integration method for free energy calculations in molecular systems. - Christopher A. Mirabzadeh; F. Marty Ytreberg (PeerJ Prepr., 2019)

Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. - Dharmeshkumar Patel; Stephanie L. Haag; Jagdish Suresh Patel; F. Marty Ytreberg; Matthew T. Bernards (J. Chem. Inf. Model., 2022)

Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability. - Yesol Sapozhnikov; Jagdish Suresh Patel; F. Marty Ytreberg; Craig R. Miller (BMC Bioinform., 2023)