William (Joe) Allen

William (Joe) Allen

Research Associate

Life Sciences Computing Group

Houston, TX

William (Joe) Allen joined the TACC Life Sciences Computing Group in 2015, and he is based out of the Texas Medical Center in Houston where he works to advance computational biology and bioinformatics research at UT system academic and health institutions. His research experience spans a range of disciplines from computer-aided design to wet lab biochemistry, with the central themes of drug discovery and investigating the complex processes that mediate biomolecule interactions. He is also interested in exploring new ways high performance computing resources can be used to answer challenging biological questions. Before joining TACC, Joe earned a B.S. in chemistry from the University of Jamestown (2006), and a Ph.D. in Biochemistry from Virginia Tech (2011). Following his Ph.D., he spent four years in a postdoctoral fellowship at Stony Brook University in the area of computational biology.

Areas of Research and Interest

  • Developing cyberinfrastructure for exploration, analysis, and visualization of biomedical data
  • Drug discovery methods, algorithms, and applications; Protein structure-function
  • Engaging and enabling researchers in life sciences computing

Current Projects

  • UTRC - effort to increase HPC adoption across 14 UT System institutions
  • CyVerse - command line tooling and tutorial development
  • RT-MRI - Automated real-time quantitative MRI cyberinfrastructure
  • DrugDiscovery@TACC - web portal for virtual screening

Selected Publications

Allen, W.J.; Fochtman, B.C.; Balius, T.E.; Rizzo, R.C. "Customizable de novo Design Strategies for DOCK: Application to HIVgp41 and Other Therapeutic Targets." J. Comput. Chem. 2017. (DOI: 10.1002/jcc.25052)

McGee Jr., T.D.; Yi, H.A.; Allen, W.J.; Jacobs, A.; Rizzo, R.C. "Structure-Based Identification of Inhibitors Targeting Obstruction of the HIVgp41 N-Heptad Repeat Trimer." Bioorg. Med. Chem. Lett. 2017, 27 (14), 3177-3184.

Gabr, R.E.; Tefera, G.B.; Allen, W.J.; Pednekar, A.S.; Narayana, P.A. "GRAPE: A Graphical Pipeline Environment for Image Analysis in Adaptive Magnetic Resonance Imaging." Int. J. Comput. Assist. Radiol. Surg. 2017, 12 (3), 449-457.

Airola, M.V.; Allen, W.J.; Pulkoski-Gross, M.J.; Obeid, L.M.; Rizzo, R.C.; Hannun, Y.A. "Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase." Structure 2015, 23 (8), 1482-1491.

Allen, W.J.; Yi, H.A.; Gochin, M.; Jacobs, A.; Rizzo, R.C. "Small Molecule Inhibitors of HIVgp41 N-heptad Repeat Trimer Formation." Bioorg. Med. Chem. Lett. 2015, 25 (14), 2853-2859.

Allen, W.J.; Balius, T.E.; Mukherjee, S.; Brozell, S.R.; Moustakas, D.T.; Lang, P.T.; Case, D.A.; Kuntz, I.D.; Rizzo, R.C. "DOCK 6: Impact of New Features and Current Docking Performance." J. Comput. Chem. 2015, 36 (15), 1132-1156.

Allen, W.J.; Wiley, M.R.; Myles, K.M.; Adelman, Z.N.; Bevan, D.R. "Steered Molecular Dynamics Identifies Critical Residues of the Nodamura Virus B2 Suppressor of RNAi." J. Mol. Model. 2014, 20 (3), 2092.

Allen, W.J.; Rizzo, R.C. "Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design." J. Chem. Inf. Model. 2014, 54 (2), 518-529.

Holden, P.M.; Allen, W.J.; Gochin, M.; Rizzo, R.C. "Strategies for Lead Discovery: Application of Footprint Similarity Targeting HIVgp41." Bioorg. Med. Chem. 2014, 22 (1), 651-661.

Furt, F.; Allen, W.J.; Widhalm, J.R.; Madzelan, P.; Rizzo, R.C.; Basset, G.; Wilson, M.A. "Functional Convergence of Structurally Distinct Thioesterases from Cyanobacteria and Plants Involved in Phylloquinone Biosynthesis." Acta Cryst. 2013, D69 (10), 1876-1888.

Balius, T.E.; Allen, W.J.; Mukherjee, S.; Rizzo, R.C. "Grid-Based Molecular Footprint Comparison Method for Docking and De Novo Design: Application to HIVgp41." J. Comput. Chem. 2013, 34 (14), 1226-1240.

Allen, W.J.; Rizzo, R.C. "Computer-Aided Approaches for Targeting HIVgp41." Biology 2012, 1 (2), 311-338.

Allen, W.J.; Bevan, D.R. "Steered Molecular Dynamics Simulations Reveal Important Mechanisms in Reversible Monoamine Oxidase B Inhibition." Biochemistry 2011, 50 (29), 6441-6454.

Grimm, M.L.; Allen, W.J.; Finn, M.; Castagnoli Jr., N.; Tanko, J.M. "Reaction of Benzophenone Triplet with Aliphatic Amines. What a Potent Neurotoxin Can Tell Us about the Reaction Mechanism." Bioorg. Med. Chem. 2011, 19 (4), 1458-1463.

Lemkul, J.A.; Allen, W.J.; Bevan, D.R. "Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies." J. Chem. Inf. Model. 2010, 50 (12), 2221-2235.

Allen, W.J.; Capelluto, D.G.S.; Finkielstein, C.V.; Bevan, D.R. "Modeling the Relationship between the p53 C-Terminal Domain and Its Binding Partners Using Molecular Dynamics." J. Phys. Chem. B 2010, 114 (41), 13201-13213.

Allen, W.J.; Lemkul, J.A.; Bevan, D.R. "GridMAT-MD: A Grid-Based Membrane Analysis Tool for Use with Molecular Dynamics." J. Comput. Chem. 2009, 30 (12), 1952-1958.

For a list of publications, please see: PubMed.


Ph.D., Biochemistry,
Virginia Tech

B.S., Chemistry,
University of Jamestown

Memberships and Affiliations

  • American Chemical Society
  • Ken Kennedy Institute