Programming Escherichia coli to function as a digital display

Autor: Jonghyeon Shin, Shuyi Zhang, Bryan S Der, Alec AK Nielsen, Christopher A Voigt

Publikováno v: Molecular Systems Biology, Vol 16, Iss 3, Pp 1-12 (2020)

Abstract Synthetic genetic circuits offer the potential to wield computational control over biology, but their complexity is limited by the accuracy of mathematical models. Here, we present advances that enable the complete encoding of an electronic

Externí odkaz: https://doaj.org/article/c282b0dbd8e74862bb4d1be005af75a5

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

Autor: Sergey Lyskov, Fang-Chieh Chou, Shane Ó Conchúir, Bryan S Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian D Weitzner, P Douglas Renfrew, Parin Sripakdeevong, Benjamin Borgo, James J Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey J Gray, Rhiju Das

Publikováno v: PLoS ONE, Vol 8, Iss 5, p e63906 (2013)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its

Externí odkaz: https://doaj.org/article/d9277b7f6a044d4fac1337487c7245fc

Computer‐based engineering of thermostabilized antibody fragments

Autor: Sang Taek Jung, George Georgiou, Chang-Han Lee, Gregory C. Ippolito, Wenzong Li, Jiwon Lee, R. E. Hughes, Oana I. Lungu, Brian Kuhlman, Bryan S. Der, Jeffrey J. Gray, Jianqing Xu, Tae Hyun Kang, Yan Zhang, Nicholas M. Marshall, Bing Tan, Christos S. Karamitros, Andrew D. Ellington, Aleksandr E. Miklos

Publikováno v: AIChE J

We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d0df86792b3cad76d308c5f997e78afa
https://doi.org/10.1002/aic.16864

Genetic circuit characterization and debugging using RNA-seq

Autor: Alec Ak Nielsen, Jing Zhang, Thomas E. Gorochowski, Yongjin Park, Bryan S. Der, Christopher A. Voigt, D. Benjamin Gordon, Amin Espah Borujeni

Publikováno v: Molecular Systems Biology
Gorochowski, T, Espah Borujeni, A, Park, Y, Nielsen, A, Zhang, J, Der, B, Gordon, D B & Voigt, C 2017, ' Genetic circuit characterization and debugging using RNA-seq ', Molecular Systems Biology, vol. 13, no. 11, 952 . https://doi.org/10.15252/msb.20167461

Genetic circuits implement computational operations within a cell. Debugging them is difficult because their function is defined by multiple states (e.g., combinations of inputs) that vary in time. Here, we develop RNA‐seq methods that enable the s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::57153c730326bed7df2526c4845928dc
https://pubmed.ncbi.nlm.nih.gov/29122925

Probing the minimal determinants of zinc binding with computational protein design

Autor: Brian Kuhlman, Bryan S. Der, Sharon L. Guffy

Publikováno v: Protein engineering, designselection : PEDS. 29(8)

Structure-based protein design tests our understanding of the minimal determinants of protein structure and function. Previous studies have demonstrated that placing zinc binding amino acids (His, Glu, Asp or Cys) near each other in a folded protein

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f919243f35c1a21eef8c909aeb0153c6
https://pubmed.ncbi.nlm.nih.gov/27358168