In Silico-Directed Evolution Using CADEE
Amrein, Beat Anton ; Runthala, Ashish and Kamerlin, Shina Caroline Lynn LU
(2019)
In Methods in molecular biology (Clifton, N.J.)
1851.
p.381-415
- Abstract
Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitates the computer-aided directed evolution of enzymes. Our initial work (Amrein et al., IUCrJ 4:50-64, 2017) presented a pedagogical example of the application of CADEE to triosephosphate isomerase, to illustrate the CADEE workflow. In this contribution, we describe this workflow in detail, including code input/output snippets, in order to allow users to set up and execute CADEE simulations on any system of interest.
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/afd0ff59-c593-48c4-b5a9-6f791de4ac7c
- author
- Amrein, Beat Anton
; Runthala, Ashish
and Kamerlin, Shina Caroline Lynn
LU
- publishing date
- 2019
- type
- Contribution to journal
- publication status
- published
- keywords
- Computational Biology/methods, Directed Molecular Evolution, Enzymes/chemistry, Protein Engineering
- in
- Methods in molecular biology (Clifton, N.J.)
- volume
- 1851
- pages
- 35 pages
- publisher
- Springer
- external identifiers
-
- scopus:85054767374
- pmid:30298410
- ISSN
- 1940-6029
- DOI
- 10.1007/978-1-4939-8736-8_22
- language
- English
- LU publication?
- no
- id
- afd0ff59-c593-48c4-b5a9-6f791de4ac7c
- date added to LUP
- 2025-01-11 20:56:26
- date last changed
- 2025-04-20 11:47:35
@article{afd0ff59-c593-48c4-b5a9-6f791de4ac7c,
abstract = {{<p>Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitates the computer-aided directed evolution of enzymes. Our initial work (Amrein et al., IUCrJ 4:50-64, 2017) presented a pedagogical example of the application of CADEE to triosephosphate isomerase, to illustrate the CADEE workflow. In this contribution, we describe this workflow in detail, including code input/output snippets, in order to allow users to set up and execute CADEE simulations on any system of interest.</p>}},
author = {{Amrein, Beat Anton and Runthala, Ashish and Kamerlin, Shina Caroline Lynn}},
issn = {{1940-6029}},
keywords = {{Computational Biology/methods; Directed Molecular Evolution; Enzymes/chemistry; Protein Engineering}},
language = {{eng}},
pages = {{381--415}},
publisher = {{Springer}},
series = {{Methods in molecular biology (Clifton, N.J.)}},
title = {{In Silico-Directed Evolution Using CADEE}},
url = {{http://dx.doi.org/10.1007/978-1-4939-8736-8_22}},
doi = {{10.1007/978-1-4939-8736-8_22}},
volume = {{1851}},
year = {{2019}},
}