Modular reweighting software for statistical mechanical analysis of biased equilibrium data. - Daniel J. Sindhikara (Comput. Phys. Commun., 2012)

Placevent: An algorithm for prediction of explicit solvent atom distribution - Application to HIV-1 protease and F-ATP synthase. - Daniel J. Sindhikara; Norio Yoshida; Fumio Hirata (J. Comput. Chem., 2012)

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. - Siegfried S. F. Leung; Daniel J. Sindhikara; Matthew P. Jacobson (J. Chem. Inf. Model., 2016)

Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling. - Daniel J. Sindhikara; Steven A. Spronk; Tyler Day; Kenneth W. Borrelli; Daniel L. Cheney; Shana L. Posy (J. Chem. Inf. Model., 2017)

Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis. - Janet L. Paulsen; Haoyu S. Yu; Dan Sindhikara; Lingle Wang; Todd Appleby; Armando G. Villaseñor; Uli Schmitz; Devleena Shivakumar (J. Chem. Inf. Model., 2020)

Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics. - Ryan Dykstra; Dan Sindhikara (J. Chem. Inf. Model., 2025)