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)

Grid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41. - Trent E. Balius; William J. Allen; Sudipto Mukherjee 002; Robert C. Rizzo (J. Comput. Chem., 2013)

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design. - William J. Allen; Robert C. Rizzo (J. Chem. Inf. Model., 2014)

DOCK 6: Impact of new features and current docking performance. - William J. Allen; Trent E. Balius; Sudipto Mukherjee 002; Scott R. Brozell; Demetri Moustakas; P. Therese Lang; David A. Case; Irwin D. Kuntz; Robert C. Rizzo (J. Comput. Chem., 2015)

GRAPE: a graphical pipeline environment for image analysis in adaptive magnetic resonance imaging. - Refaat E. Gabr; Getaneh B. Tefera; William J. Allen; Amol S. Pednekar; Ponnada A. Narayana (Int. J. Comput. Assist. Radiol. Surg., 2017)

Erratum to: GRAPE: a graphical pipeline environment for image analysis in adaptive magnetic resonance imaging. - Refaat E. Gabr; Getaneh B. Tefera; William J. Allen; Amol S. Pednekar; Ponnada A. Narayana (Int. J. Comput. Assist. Radiol. Surg., 2017)

Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. - William J. Allen; Brian C. Fochtman; Trent E. Balius; Robert C. Rizzo (J. Comput. Chem., 2017)

Platform for Automated Real-Time High Performance Analytics on Medical Image Data. - William J. Allen; Refaat E. Gabr; Getaneh B. Tefera; Amol S. Pednekar; Matthew W. Vaughn; Ponnada A. Narayana (IEEE J. Biomed. Health Informatics, 2018)

Tetrahedral mesh deformation with positional constraints. - Wenjing Zhang 009; Yuewen Ma; Jianmin Zheng; William J. Allen (Comput. Aided Geom. Des., 2020)

Role of alkylated residues in the tetrapeptide self-assembly - A molecular dynamics study. - Rajarajeswari Muthusivarajan; William J. Allen; Ashok D. Pehere; Konstantin V. Sokolov; David Fuentes 001 (J. Comput. Chem., 2020)

BiasNet: A Model to Predict Ligand Bias Toward GPCR Signaling. - Jason E. Sanchez; Govinda B. Kc; Julian Franco; William J. Allen; Jesus David Garcia; Suman Sirimulla (J. Chem. Inf. Model., 2021)

Containerizing Visualization Software: Experiences and Best Practices. - Andrew J. Solis; William J. Allen; Erik S. Ferlanti (PEARC, 2022)

A molecular evolution algorithm for ligand design in DOCK. - Lauren E. Prentis; Courtney D. Singleton; John D. Bickel; William J. Allen; Robert C. Rizzo (J. Comput. Chem., 2022)

Perspectives and Experiences Supporting Containers for Research Computing at the Texas Advanced Computing Center. - Erik S. Ferlanti; William J. Allen; Ernesto A. B. F. Lima; Yinzhi Wang; John M. Fonner (SC Workshops, 2023)

Scalable and Reproducible Virtual Screening through an API-Integrated Workflow. - Tiffany Huff; Austin Darrow; Joshua Medina; Erik S. Ferlanti; James D. Carson; John M. Fonner; Sal Tijerina; Stanley J. Watowich; William J. Allen (PEARC, 2023)