Silva, Daniel-Adriano

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 888

De novo design of potent and selective mimics of IL-2 and IL-15

Silva, D.-A., Yu, S., Ulge, U. Y., Spangler, J. B., Jude, K. M., Labão-Almeida, C., Ali, L. R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., et al. (2019) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 531

Massively parallel de novo protein design for targeted therapeutics

Chevalier, A., Silva, D.-A., Rocklin, G. J., Hicks, D. R., Vergara, R., Murapa, P., Bernard, S. M., Zhang, L., Lam, K.-H., Yao, G., et al. (2017) · Nature

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 453

De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2

Linsky, T. W., Vergara, R., Codina, N., Nelson, J. W., Walker, M. J., Su, W., Barnes, C. O., Hsiang, T.-Y., Esser-Nobis, K., Yu, K., et al. (2020) · Science

SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approaches

Cited by 216

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

Zhuang, W., Cui, R. Z., Silva, D.-A., & Huang, X. (2011) · The Journal of Physical Chemistry B

Protein Structure and DynamicsSpectroscopy and Quantum Chemical Studies

Cited by 70

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

Yao, Y., Cui, R. Z., Bowman, G. R., Silva, D.-A., Sun, J., & Huang, X. (2013) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 69