Bookshelf: a simple curation system for the storage of biomolecular simulation data. - Shabana Vohra; Benjamin A. Hall; Daniel A. Holdbrook; Syma Khalid; Philip C. Biggin (Database J. Biol. Databases Curation, 2010)

Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study. - Nils A. Berglund; Thomas J. Piggot; Damien Jefferies; Richard B. Sessions; Peter J. Bond; Syma Khalid (PLoS Comput. Biol., 2015)

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. - Pin-Chia Hsu; Bart M. H. Bruininks; Damien Jefferies; Paulo C. T. Souza; Jumin Lee; Dhilon S. Patel; Siewert J. Marrink; Yifei Qi; Syma Khalid; Wonpil Im (J. Comput. Chem., 2017)

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. - James A. Graham; Jonathan W. Essex; Syma Khalid (J. Chem. Inf. Model., 2017)

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. - Lorenzo Casalino; Abigail C. Dommer; Zied Gaieb; Emília P. Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony T. Bogetti; Austin Clyde; Heng Ma; Hyungro Lee; et al. (Int. J. High Perform. Comput. Appl., 2021)

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. - Ya Gao 004; Jumin Lee; Iain Peter Shand Smith; Hwayoung Lee; Seonghoon Kim; Yifei Qi; Jeffery B. Klauda; Göran Widmalm; Syma Khalid; Wonpil Im (J. Chem. Inf. Model., 2021)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. - Kahlan E. Newman; Syma Khalid (PLoS Comput. Biol., 2023)

Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field. - Astrid F. Brandner; Iain Peter Shand Smith; Siewert J. Marrink; Paulo C. T. Souza; Syma Khalid (J. Chem. Inf. Model., 2025)