DNAssembly Modular Cloning Plasmid Database
Web interface to automate high-throughput assembly, annotation, and tracking of modular cloning plasmids
Posts by Collection
portfolio
DNAssembly Python Package
High-throughput plasmid assembly with Python
PyRosetta Interactive Labs
Jupyter notebooks for teaching essential protein design concepts
publications
Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2‐dehydrogenase
Published in Protein Science, 2015
Experimentally determined the contributions of active site residues toward catalysis
Recommended citation: Lucas, J.E. and Siegel, J.B. (2015), Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2‐dehydrogenase. Protein Science, 24: 936-945. doi:10.1002/pro.2669 https://onlinelibrary.wiley.com/doi/full/10.1002/pro.2669
Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation
Published in The Journal of Physical Chemistry B, 2018
Improving our ability to calculate protein-protein interface DDGs upon mutation
Recommended citation: Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B. 2018 doi: 10.1021/acs.jpcb.7b11367. https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b11367
Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs
Published in Nature Communications, 2019
Developing ligand-inducible sgRNAs to modulate Cas9 activity
Recommended citation: Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 May 9;10(1):2127. doi: 10.1038/s41467-019-09985-2. https://www.nature.com/articles/s41467-019-09985-2
New Protein Design Methods for De Novo Small Molecule Binding Sites
Published in PLoS Computational Biology, 2020
Leveraging the PDB to inform de novo small molecule binding site design
Recommended citation: Lucas JE, Kortemme T (2020) New computational protein design methods for de novo small molecule binding sites. PLOS Computational Biology 16(10): e1008178. https://doi.org/10.1371/journal.pcbi.1008178 https://doi.org/10.1371/journal.pcbi.1008178
talks
De Novo Ligand Binding Site Design for Improved Biosensors
Published:
I was invited to give a lightning talk on my work applying my de novo binding site design method to engineering new chemically-induced dimerization systems. I also presented a poster on my work at this event.
De Novo Ligand Binding Site Design for Improved Biosensors
Published:
I present my work developing a new method to build small molecule binding sites from scratch. I applied my method to introduce binding sites into protein-protein interfaces to create new chemically-induced dimerization systems.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.