M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. - Brian G. Pierce; Weiwei Tong; Zhiping Weng (Bioinform., 2005)

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. - Jie Wang; Jiali Zhuang; Sowmya Iyer; Xin-Ying Lin; Melissa C. Greven; Bong-Hyun Kim; Jill Moore; Brian G. Pierce; Xianjun Dong; Daniel Virgil; Ewan Birney; Jui-Hung Hung; et al. (Nucleic Acids Res., 2013)

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)

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. - Brian G. Pierce; Lance M. Hellman; Moushumi Hossain; Nishant K. Singh; Craig W. Vander Kooi; Zhiping Weng; Brian M. Baker (PLoS Comput. Biol., 2014)

TCRmodel: high resolution modeling of T cell receptors from sequence. - Ragul Gowthaman; Brian G. Pierce (Nucleic Acids Res., 2018)

TCR3d: The T cell receptor structural repertoire database. - Ragul Gowthaman; Brian G. Pierce (Bioinform., 2019)

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)

CoV3D: a database of high resolution coronavirus protein structures. - Ragul Gowthaman; Johnathan D. Guest; Rui Yin 004; Jared Adolf-Bryfogle; William R. Schief; Brian G. Pierce (Nucleic Acids Res., 2021)

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants. - Rui Yin 004; Johnathan D. Guest; Ghazaleh Taherzadeh; Ragul Gowthaman; Ipsa Mittra; Jane Quackenbush; Brian G. Pierce (PLoS Comput. Biol., 2021)

TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning. - Rui Yin 004; Helder Veras Ribeiro filho; Valerie Lin; Ragul Gowthaman; Melyssa Cheung; Brian G. Pierce (Nucleic Acids Res., 2023)

Exploring the potential of structure-based deep learning approaches for T cell receptor design. - Helder Veras Ribeiro filho; Gabriel Ernesto Jara; João Victor da Silva Guerra; Melyssa Cheung; Nathaniel R. Felbinger; José Geraldo de Carvalho Pereira; Brian G. Pierce; Paulo Sérgio Lopes-de-Oliveira (PLoS Comput. Biol., 2024)