Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Tamuka M. Chidyausiku"'
Autor:
Tamuka M. Chidyausiku, Soraia R. Mendes, Jason C. Klima, Marta Nadal, Ulrich Eckhard, Jorge Roel-Touris, Scott Houliston, Tibisay Guevara, Hugh K. Haddox, Adam Moyer, Cheryl H. Arrowsmith, F. Xavier Gomis-Rüth, David Baker, Enrique Marcos
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-14 (2022)
The immunoglobulin domain framework of antibodies has been a long standing design challenge. Here, the authors describe design rules for tailoring these domains and show they can be accurately designed, de novo, with high stability and the ability to
Externí odkaz:
https://doaj.org/article/97a8dd6f14d04e56ae09b84b09e5515d
Autor:
Jedediah M. Singer, Scott Novotney, Devin Strickland, Hugh K. Haddox, Nicholas Leiby, Gabriel J. Rocklin, Cameron M. Chow, Anindya Roy, Asim K. Bera, Francis C. Motta, Longxing Cao, Eva-Maria Strauch, Tamuka M. Chidyausiku, Alex Ford, Ethan Ho, Alexander Zaitzeff, Craig O. Mackenzie, Hamed Eramian, Frank DiMaio, Gevorg Grigoryan, Matthew Vaughn, Lance J. Stewart, David Baker, Eric Klavins
Publikováno v:
PLoS ONE, Vol 17, Iss 3 (2022)
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be
Externí odkaz:
https://doaj.org/article/6bc977c80731465da8bb65f2719bfb0c
Autor:
David Baker, Gaetano T. Montelione, T.A. Ramelot, Tamuka M. Chidyausiku, Jingzhou Hao, Alex Kang, Samuel J. Pellock, Lauren Carter, Christoffer Norn, Ivan Anishchenko, Frank DiMaio, Khushboo Bafna, Sergey Ovchinnikov, Asim K. Bera, Cameron M. Chow
Publikováno v:
Nature
There has been considerable recent progress in protein structure prediction using deep neural networks to predict inter-residue distances from amino acid sequences1–3. Here we investigate whether the information captured by such networks is suffici
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c1baf935a548717fb6685bb5aec553e
https://europepmc.org/articles/PMC9293396/
https://europepmc.org/articles/PMC9293396/
Autor:
Jedediah M. Singer, Scott Novotney, Devin Strickland, Hugh K. Haddox, Nicholas Leiby, Gabriel J. Rocklin, Cameron M. Chow, Anindya Roy, Asim K. Bera, Francis C. Motta, Longxing Cao, Eva-Maria Strauch, Tamuka M. Chidyausiku, Alex Ford, Ethan Ho, Alexander Zaitzeff, Craig O. Mackenzie, Hamed Eramian, Frank DiMaio, Gevorg Grigoryan, Matthew Vaughn, Lance J. Stewart, David Baker, Eric Klavins
Publikováno v:
PloS one. 17(3)
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::399565bf5a83555fbb2550c6932ae47b
https://pubmed.ncbi.nlm.nih.gov/35286324
https://pubmed.ncbi.nlm.nih.gov/35286324
Autor:
Devin Strickland, Alex Ford, Tamuka M. Chidyausiku, Francis C. Motta, Hamed Eramian, Gabriel J. Rocklin, Jedediah M. Singer, Longxing Cao, Ethan Ho, Anindya Roy, Gevorg Grigoryan, Scott Novotney, Asim K. Bera, Eva-Maria Strauch, Nicholas Leiby, Cameron M. Chow, Hugh K. Haddox, David Baker, Lance Stewart, Matthew W. Vaughn, Craig O. Mackenzie, Frank DiMaio, Eric Klavins
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::1e9365315f7ac752b3e51cd28d482387
https://doi.org/10.1101/2021.03.12.435185
https://doi.org/10.1101/2021.03.12.435185
There has been considerable recent progress in protein structure prediction using deep neural networks to infer distance constraints from amino acid residue co-evolution1–3. We investigated whether the information captured by such networks is suffi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5c31bf20d5e935301aa6c83bee8e504a
https://doi.org/10.1101/2020.07.22.211482
https://doi.org/10.1101/2020.07.22.211482
Autor:
Gustav Oberdorfer, Santrupti Nerli, David Baker, Lauren Carter, Konstantinos Tripsianes, Nikolaos G. Sgourakis, Andrew C. McShan, Lucas G. Nivón, Enrique Marcos, Tamuka M. Chidyausiku, Audrey Davis, Thomas Evangelidis
Publikováno v:
Nature structural & molecular biology
β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-β-sheet proteins from first principles lags far behind the design of all-α
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::21b68551131c2cbeda9fd08b000bcb3a
http://europepmc.org/articles/PMC6219906
http://europepmc.org/articles/PMC6219906
Autor:
Scott Houliston, Gabriel J. Rocklin, Alex Ford, Tamuka M. Chidyausiku, David Baker, Alexander Lemak, Rashmi Ravichandran, Aaron Chevalier, Cheryl H. Arrowsmith, Lauren Carter, Vikram Khipple Mulligan, Inna Goreshnik
Publikováno v:
Science. 357:168-175
Exploring structure space to understand stability Understanding the determinants of protein stability is challenging because native proteins have conformations that are optimized for function. Proteins designed without functional bias could give insi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::358d1bac73ef9dd37514e225d2c9f264
https://doi.org/10.1126/science.aan0693
https://doi.org/10.1126/science.aan0693
Autor:
Gustav Oberdorfer, Rong Xiao, Benjamin Basanta, Daniel-Adriano Silva, Banumathi Sankaran, Enrique Marcos, Gaohua Liu, Rongjin Guan, Jose Henrique Pereira, Gaetano T. Montelione, Tamuka M. Chidyausiku, Jiayi Dou, David Baker, Yuefeng Tang, G. V. T. Swapna, Peter H. Zwart
Publikováno v:
Science. 355:201-206
Designing proteins with cavities In de novo protein design, creating custom-tailored binding sites is a particular challenge because these sites often involve nonideal backbone structures. For example, curved b sheets are a common ligand binding moti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::40fee17a5a1d6dc88d3017315bbde948
https://doi.org/10.1126/science.aah7389
https://doi.org/10.1126/science.aah7389
Autor:
Gabriel J. Rocklin, Cheryl H. Arrowsmith, David Baker, Alex Ford, Tamuka M. Chidyausiku, Inna Goreshnik, Scott Houliston
Publikováno v:
Biophysical Journal. 112:194a
Despite two decades of progress in computational protein design, a large fraction of de novo designed proteins fail to fold as designed due to our incomplete understanding of the principles governing protein stability. These challenges persist in par
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::bd9a3672e9dfb31977bfa6563920e593
https://doi.org/10.1016/j.bpj.2016.11.1076
https://doi.org/10.1016/j.bpj.2016.11.1076