Zobrazeno 1 - 10
of 26
pro vyhledávání: '"Daniel J. Diaz"'
Autor:
Daniel J. Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M. Loy, Jordan Wells, David Yang, Andrew D. Ellington, Alexandros G. Dimakis, Adam R. Klivans
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)
Abstract Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph-transformer framework that achieves SOTA performance on accu
Externí odkaz:
https://doaj.org/article/09e8ba873c164e1eb910e28fd655392f
Autor:
Simon d’Oelsnitz, Daniel J. Diaz, Wantae Kim, Daniel J. Acosta, Tyler L. Dangerfield, Mason W. Schechter, Matthew B. Minus, James R. Howard, Hannah Do, James M. Loy, Hal S. Alper, Y. Jessie Zhang, Andrew D. Ellington
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)
Abstract A major challenge to achieving industry-scale biomanufacturing of therapeutic alkaloids is the slow process of biocatalyst engineering. Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are complex plant secondary m
Externí odkaz:
https://doaj.org/article/a590be639471443d8f68f7c532e9fc11
Autor:
Anastasiya V. Kulikova, Daniel J. Diaz, Tianlong Chen, T. Jeffrey Cole, Andrew D. Ellington, Claus O. Wilke
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-9 (2023)
Abstract Deep learning models are seeing increased use as methods to predict mutational effects or allowed mutations in proteins. The models commonly used for these purposes include large language models (LLMs) and 3D Convolutional Neural Networks (C
Externí odkaz:
https://doaj.org/article/de2a0e4bd981453f829bc025b68f3554
Publikováno v:
ACS Synthetic Biology. 11:3534-3537
Genetic biosensors are integral to synthetic biology. In particular, ligand-inducible prokaryotic transcription factors are frequently used in high-throughput screening, for dynamic feedback regulation, as multilayer logic gates, and in diagnostic ap
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce8a8c52187fbbb66749fae3693d2dd8
https://doi.org/10.1021/acssynbio.2c00382
https://doi.org/10.1021/acssynbio.2c00382
Autor:
Daniel J. Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M. Loy, Jordan Wells, David Yang, Andrew D. Ellington, Alex Dimakis, Adam R. Klivans
Stabilizing proteins is a fundamental challenge in protein engineering and is almost always a prerequisite for the development of industrial and pharmaceutical biotechnologies. Here we present Stability Oracle: a structure-based graph-transformer fra
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7e0c67e32a0c27baf221dc7362b72e04
https://doi.org/10.1101/2023.05.15.540857
https://doi.org/10.1101/2023.05.15.540857
Autor:
Inyup, Paik, Phuoc H T, Ngo, Raghav, Shroff, Daniel J, Diaz, Andre C, Maranhao, David J F, Walker, Sanchita, Bhadra, Andrew D, Ellington
Publikováno v:
Biochemistry
The DNA polymerase I from Geobacillus stearothermophilus (also known as Bst DNAP) is widely used in isothermal amplification reactions, where its strand displacement ability is prized. More robust versions of this enzyme should be enabled for diagnos
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::8764414f6e516fa3e1091f62c4301641
https://pubmed.ncbi.nlm.nih.gov/34762799
https://pubmed.ncbi.nlm.nih.gov/34762799
Autor:
Anastasiya V. Kulikova, Daniel J. Diaz, Tianlong Chen, T. Jeffrey Cole, Andrew D. Ellington, Claus O. Wilke
Publikováno v:
bioRxiv
Deep learning models are seeing increased use as methods to predict mutational effects or allowed mutations at various sites in proteins. The models commonly used for these purposes include large language models (LLMs) and 3D Convolutional Neural Net
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c600fb0dd976659284d61586dad08097
https://doi.org/10.1101/2023.03.20.533508
https://doi.org/10.1101/2023.03.20.533508
Autor:
Hongyuan Lu, Daniel J. Diaz, Natalie J. Czarnecki, Congzhi Zhu, Wantae Kim, Raghav Shroff, Daniel J. Acosta, Bradley R. Alexander, Hannah O. Cole, Yan Zhang, Nathaniel A. Lynd, Andrew D. Ellington, Hal S. Alper
Publikováno v:
Nature. 604:662-667
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e2049a66f8a6e44b97b3659af01e1d4d
https://doi.org/10.1038/s41586-022-04599-z
https://doi.org/10.1038/s41586-022-04599-z
Publikováno v:
Analysis & Sensing. 3
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6f8018f6c78b7d091ee60f70f46f27d2
https://doi.org/10.1002/anse.202200095
https://doi.org/10.1002/anse.202200095
Autor:
Raghav Shroff, Phuoc H. T. Ngo, Daniel J. Diaz, Sanchita Bhadra, Andrew D. Ellington, Andre C. Maranhao, Inyup Paik, David J. F. Walker
Publikováno v:
Biochemistry. 62:410-418
The DNA polymerase I from Geobacillus stearothermophilus (also known as Bst DNAP) is widely used in isothermal amplification reactions, where its strand displacement ability is prized. More robust versions of this enzyme should be enabled for diagnos
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ed3c1631add22c8a621d58b8a3ccdc9f
https://doi.org/10.1021/acs.biochem.1c00451
https://doi.org/10.1021/acs.biochem.1c00451