| DOCK 6: impact of new features and current docking performance WJ Allen, TE Balius, S Mukherjee, SR Brozell, DT Moustakas, PT Lang, ... Journal of computational chemistry 36 (15), 1132-1156, 2015 | 727 | 2015 |
| GridMAT‐MD: A grid‐based membrane analysis tool for use with molecular dynamics WJ Allen, JA Lemkul, DR Bevan Journal of computational chemistry 30 (12), 1952-1958, 2009 | 318 | 2009 |
| Practical considerations for building GROMOS-compatible small-molecule topologies JA Lemkul, WJ Allen, DR Bevan Journal of chemical information and modeling 50 (12), 2221-2235, 2010 | 228 | 2010 |
| Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design WJ Allen, RC Rizzo Journal of chemical information and modeling 54 (2), 518-529, 2014 | 106 | 2014 |
| Brain and lesion segmentation in multiple sclerosis using fully convolutional neural networks: A large-scale study RE Gabr, I Coronado, M Robinson, SJ Sujit, S Datta, X Sun, WJ Allen, ... Multiple Sclerosis Journal 26 (10), 1217-1226, 2020 | 78 | 2020 |
| Structural basis for ceramide recognition and hydrolysis by human neutral ceramidase MV Airola, WJ Allen, MJ Pulkoski-Gross, LM Obeid, RC Rizzo, YA Hannun Structure 23 (8), 1482-1491, 2015 | 46 | 2015 |
| Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets WJ Allen, BC Fochtman, TE Balius, RC Rizzo Journal of computational chemistry 38 (30), 2641-2663, 2017 | 41 | 2017 |
| Grid‐based molecular footprint comparison method for docking and de novo design: Application to HIVgp41 TE Balius, WJ Allen, S Mukherjee, RC Rizzo Journal of computational chemistry 34 (14), 1226-1240, 2013 | 40 | 2013 |
| Steered molecular dynamics simulations reveal important mechanisms in reversible monoamine oxidase B inhibition WJ Allen, DR Bevan Biochemistry 50 (29), 6441-6454, 2011 | 32 | 2011 |
| Small molecule inhibitors of HIVgp41 N-heptad repeat trimer formation WJ Allen, HA Yi, M Gochin, A Jacobs, RC Rizzo Bioorganic & medicinal chemistry letters 25 (14), 2853-2859, 2015 | 25 | 2015 |
| Strategies for lead discovery: Application of footprint similarity targeting HIVgp41 PM Holden, WJ Allen, M Gochin, RC Rizzo Bioorganic & medicinal chemistry 22 (1), 651-661, 2014 | 25 | 2014 |
| Modeling the relationship between the p53 C-terminal domain and its binding partners using molecular dynamics WJ Allen, DGS Capelluto, CV Finkielstein, DR Bevan The Journal of Physical Chemistry B 114 (41), 13201-13213, 2010 | 24 | 2010 |
| Computer-aided approaches for targeting HIVgp41 WJ Allen, RC Rizzo Biology 1 (2), 311-338, 2012 | 22 | 2012 |
| Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi WJ Allen, MR Wiley, KM Myles, ZN Adelman, DR Bevan Journal of molecular modeling 20 (3), 2092, 2014 | 15 | 2014 |
| Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer TD McGee Jr, HA Yi, WJ Allen, A Jacobs, RC Rizzo Bioorganic & medicinal chemistry letters 27 (14), 3177-3184, 2017 | 14 | 2017 |
| A molecular evolution algorithm for ligand design in DOCK LE Prentis, CD Singleton, JD Bickel, WJ Allen, RC Rizzo Journal of Computational Chemistry 43 (29), 1942-1963, 2022 | 9 | 2022 |
| A molecular dynamics approach towards evaluating osmotic and thermal stress in the extracellular environment D Fuentes, NM Muñoz, C Guo, U Polak, AA Minhaj, WJ Allen, MC Gustin, ... International Journal of Hyperthermia 35 (1), 559-567, 2019 | 9 | 2019 |
| Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis F Furt, WJ Allen, JR Widhalm, P Madzelan, RC Rizzo, G Basset, ... Acta Crystallographica Section D: Biological Crystallography 69 (10), 1876-1888, 2013 | 8 | 2013 |
| BiasNet: A Model to Predict Ligand Bias Toward GPCR Signaling JE Sanchez, GB Kc, J Franco, WJ Allen, JD Garcia, S Sirimulla Journal of Chemical Information and Modeling 61 (9), 4190-4199, 2021 | 7 | 2021 |
| GRAPE: a graphical pipeline environment for image analysis in adaptive magnetic resonance imaging RE Gabr, GB Tefera, WJ Allen, AS Pednekar, PA Narayana International journal of computer assisted radiology and surgery 12, 449-457, 2017 | 6 | 2017 |
