Docking-MM-GB/SA and ADME Screening of HIV-1 NNRTI Inhibitor: Nevirapine and its Analogues. - Dipankar Sengupta; Deeptak Verma; Pradeep Kumar Naik (Silico Biol., 2008)

WaveMap: Interactively Discovering Features From Protein Flexibility Matrices Using Wavelet-based Visual Analytics. - Scott Barlowe; Yujie Liu 009; Jing Yang 001; Dennis R. Livesay; Donald J. Jacobs; James Mottonen; Deeptak Verma (Comput. Graph. Forum, 2011)

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. - Deeptak Verma; Donald J. Jacobs; Dennis R. Livesay (PLoS Comput. Biol., 2012)

A visual analytics approach to exploring protein flexibility subspaces. - Scott Barlowe; Jing Yang 001; Donald J. Jacobs; Dennis R. Livesay; Jamal Alsakran; Ye Zhao 003; Deeptak Verma; James Mottonen (PacificVis, 2013)

Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity. - Deeptak Verma; Donald J. Jacobs; Dennis R. Livesay (PLoS Comput. Biol., 2013)

OCoM-SOCoM: Combinatorial Mutagenesis Library Design Optimally Combining Sequence and Structure Information. - Deeptak Verma; Gevorg Grigoryan; Chris Bailey-Kellogg (BCB, 2016)

Pareto Optimization of Combinatorial Mutagenesis Libraries. - Deeptak Verma; Gevorg Grigoryan; Chris Bailey-Kellogg (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Deep Dive into Machine Learning Models for Protein Engineering. - Yuting Xu; Deeptak Verma; Robert P. Sheridan; Andy Liaw; Junshui Ma; Nicholas M. Marshall; John McIntosh; Edward C. Sherer; Vladimir Svetnik; Jennifer M. Johnston (J. Chem. Inf. Model., 2020)

Building blocks and blueprints for bacterial autolysins. - Spencer J. Mitchell; Deeptak Verma; Karl E. Griswold; Chris Bailey-Kellogg (PLoS Comput. Biol., 2021)