On the application of the IMOMO (integrated molecular orbital + molecular orbital) method. - Thom Vreven; Keiji Morokuma (J. Comput. Chem., 2000)

Model studies of the structures, reacitivities, and reaction mechanisms of metalloenzymes. - Keiji Morokuma; Djamaladdin G. Musaev; Thom Vreven; Harold Basch; Maricel Torrent; Dmitry V. Khoroshun (IBM J. Res. Dev., 2001)

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. - Thom Vreven; Keiji Morokuma; Ödön Farkas; H. Bernhard Schlegel; Michael J. Frisch (J. Comput. Chem., 2003)

Evaluating template-based and template-free protein-protein complex structure prediction. - Thom Vreven; Howook Hwang; Brian G. Pierce; Zhiping Weng (Briefings Bioinform., 2014)

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. - Brian G. Pierce; Kevin Wiehe; Howook Hwang; Bong-Hyun Kim; Thom Vreven; Zhiping Weng (Bioinform., 2014)

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. - Brian G. Pierce; Thom Vreven; Zhiping Weng (BMC Bioinform., 2014)

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. - Iain H. Moal; Didier Barradas-Bautista; Brian Jiménez-García; Mieczyslaw Torchala; Arjan van der Velde; Thom Vreven; Zhiping Weng; Paul A. Bates; Juan Fernández-Recio (Bioinform., 2017)

Computational investigation into the fluorescence of luciferin analogues. - Thom Vreven; Stephen C. Miller (J. Comput. Chem., 2019)

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. - Sweta Vangaveti; Thom Vreven; Yang Zhang 040; Zhiping Weng (Bioinform., 2020)

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. - Tyler Borrman; Brian G. Pierce; Thom Vreven; Brian M. Baker; Zhiping Weng (Bioinform., 2021)