GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics. - William J. Allen; Justin A. Lemkul; David R. Bevan (J. Comput. Chem., 2009)

Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies. - Justin A. Lemkul; William J. Allen; David R. Bevan (J. Chem. Inf. Model., 2010)

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. - Justin A. Lemkul; Benoît Roux; David van der Spoel; Alexander D. MacKerell Jr. (J. Comput. Chem., 2015)

DIRECT-ID: An automated method to identify and quantify conformational variations - application to β2-adrenergic GPCR. - Sirish Kaushik Lakkaraju; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr. (J. Comput. Chem., 2016)

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. - Jing Huang 004; Justin A. Lemkul; Peter K. Eastman; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Polarizable force field for RNA based on the classical drude oscillator. - Justin A. Lemkul; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Integrating Scientific Programming in Communities of Practice for Students in the Life Sciences. - Alexa M. Salsbury; Anne M. Brown; Justin A. Lemkul (PEARC, 2019)

Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field. - Brian D. Ratnasinghe; Alexa M. Salsbury; Justin A. Lemkul (J. Chem. Inf. Model., 2020)

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. - Abhishek A. Kognole; Jumin Lee; Sang-Jun Park; Sunhwan Jo; Payal Chatterjee; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr.; Wonpil Im (J. Comput. Chem., 2022)

TUPÃ: Electric field analyses for molecular simulations. - Marcelo Depólo Polêto; Justin A. Lemkul (J. Comput. Chem., 2022)

charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS. - András F. Wacha; Justin A. Lemkul (J. Chem. Inf. Model., 2023)

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. - Marcelo Depólo Polêto; Justin A. Lemkul (J. Chem. Inf. Model., 2023)