A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein. - Daniel-Adriano Silva; Gregory R. Bowman; Alejandro Sosa-Peinado; Xuhui Huang (PLoS Comput. Biol., 2011)

Force field development for cofactors in the photosystem II. - Lu Zhang; Daniel-Adriano Silva; YiJing Yan; Xuhui Huang (J. Comput. Chem., 2012)

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis. - Shuo Gu; Daniel-Adriano Silva; Luming Meng; Alexander Yue; Xuhui Huang (PLoS Comput. Biol., 2014)

Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes. - Lu Zhang; Daniel-Adriano Silva; Fátima Pardo Avila; Dong Wang; Xuhui Huang (PLoS Comput. Biol., 2015)

Massively parallel de novo protein design for targeted therapeutics. - Aaron Chevalier; Daniel-Adriano Silva; Gabriel J. Rocklin; Derrick R. Hicks; Renan Vergara; Patience Murapa; Steffen M. Bernard; Lu Zhang; Kwok-Ho Lam; Guorui Yao; Christopher D. Bahl; Shin-Ichiro Miyashita; et al. (Nat., 2017)

De novo protein design by citizen scientists. - Brian Koepnick; Jeff Flatten; Tamir Husain; Alex Ford; Daniel-Adriano Silva; Matthew J. Bick; Aaron Bauer 002; Gaohua Liu; Yojiro Ishida; Alexander Boykov; Roger D. Estep; Susan Kleinfelter; et al. (Nat., 2019)

De novo design of potent and selective mimics of IL-2 and IL-15. - Daniel-Adriano Silva; Shawn Yu; Umut Y. Ulge; Jamie B. Spangler; Kevin M. Jude; Carlos Labão-Almeida; Lestat R. Ali; Alfredo Quijano-Rubio; Mikel Ruterbusch; Isabel Leung; Tamara Biary; Stephanie J. Crowley; et al. (Nat., 2019)