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Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors (2019)
Journal Article
Sartori, G. R., Leitão, A., Montanari, C. A., & Laughton, C. A. (2019). Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors. PLoS ONE, 14(12), Article e0222055. https://doi.org/10.1371/journal.pone.0222055

Cruzain, a cysteine protease of Trypanosoma cruzi, is a validated target for the treatment of Chagas disease. Due to its high similarity in three-dimensional structure with human cathepsins and their sequence identity above 70% in the active site reg... Read More about Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors.

Principal nested shape space analysis of molecular dynamics data (2019)
Journal Article
Dryden, I. L., Kim, K., Laughton, C. A., & Le, H. (2019). Principal nested shape space analysis of molecular dynamics data. Annals of Applied Statistics, 13(4), 2213-2234. https://doi.org/10.1214/19-AOAS1277

Molecular dynamics simulations produce huge datasets of temporal sequences of molecules. It is of interest to summarize the shape evolution of the molecules in a succinct, low-dimensional representation. However, Euclidean techniques such as principa... Read More about Principal nested shape space analysis of molecular dynamics data.

Poly(triazolyl methacrylate) glycopolymers as potential targeted unimolecular nanocarriers (2019)
Journal Article
Madeira Do O, J., Foralosso, R., Yilmaz, G., Mastrotto, F., King, P. J. S., Xerri, R. M., …Mantovani, G. (2019). Poly(triazolyl methacrylate) glycopolymers as potential targeted unimolecular nanocarriers. Nanoscale, 11(44), 21155-21166. https://doi.org/10.1039/C9NR05836B

Synthetic glycopolymers are increasingly investigated as multivalent ligands for a range of biological and biomedical applications. This study indicates that glycopolymers with fine-tuned balance between hydrophilic sugar pendant units and relatively... Read More about Poly(triazolyl methacrylate) glycopolymers as potential targeted unimolecular nanocarriers.

Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application (2019)
Journal Article
Meletiou, A., Gebbie-Rayet, J., & Laughton, C. (2019). Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application. Journal of Chemical Information and Modeling, 59(8), 3359-3364. https://doi.org/10.1021/acs.jcim.9b00351

The configuration of most current academic high-performance computing (HPC) resources tends to enforce ways of working with, and thinking about, molecular dynamics (MD) simulations that are not always optimal. For example, when the aim of the simulat... Read More about Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application.

CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space (2019)
Journal Article
Shkurti, A., Styliari, I. D., Balasubramanian, V., Bethune, I., Pedebos, C., Jha, S., & Laughton, C. A. (2019). CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space. Journal of Chemical Theory and Computation, 15(4), 2587-2596. https://doi.org/10.1021/acs.jctc.8b00657

© 2019 American Chemical Society. CoCo ("complementary coordinates") is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally for the investigation of NMR data. Here we investigate the potential of... Read More about CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.