Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. - Jake Gunn Glanville; Dan Kirshner 001; Nandini Krishnamurthy; Kimmen Sjölander (Nucleic Acids Res., 2007)

Catalytic site identification - a web server to identify catalytic site structural matches throughout PDB. - Daniel A. Kirshner; Jerome P. Nilmeier; Felice C. Lightstone (Nucleic Acids Res., 2013)

Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. - Derek Jones; Hyojin Kim 001; Xiaohua Zhang; Adam T. Zemla; Garrett Stevenson; William D. Bennett; Dan Kirshner 001; Sergio Ernesto Wong; Felice C. Lightstone; Jonathan E. Allen (CoRR, 2020)

High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models. - Garrett A. Stevenson; Derek Jones; Hyojin Kim 001; W. F. Drew Bennett; Brian J. Bennion; Monica Borucki; Feliza Bourguet; Aidan Epstein; Magdalena Franco; Brooke Harmon; Stewart He; Max P. Katz; et al. (SC, 2021)

Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. - Derek Jones; Hyojin Kim 001; Xiaohua Zhang; Adam T. Zemla; Garrett Stevenson; W. F. Drew Bennett; Daniel A. Kirshner; Sergio Ernesto Wong; Felice C. Lightstone; Jonathan E. Allen (J. Chem. Inf. Model., 2021)

Scalable Composition and Analysis Techniques for Massive Scientific Workflows. - Dong H. Ahn; Xiaohua Zhang; Jeffrey Mast; Stephen Herbein; Francesco Di Natale; Dan Kirshner 001; Sam Ade Jacobs; Ian Karlin; Daniel J. Milroy; Bronis R. de Supinski; Brian Van Essen; Jonathan E. Allen; et al. (e-Science, 2022)

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. - Garrett A. Stevenson; Dan Kirshner 001; Brian J. Bennion; Yue Yang; Xiaohua Zhang; Adam T. Zemla; Marisa W. Torres; Aidan Epstein; Derek Jones; Hyojin Kim 001; W. F. Drew Bennett; Sergio Ernesto Wong; et al. (J. Chem. Inf. Model., 2023)