Jonathan D Tyzack
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Explore the profile of Jonathan D Tyzack including associated specialties, affiliations and a list of published articles.
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24
Citations
410
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Recent Articles
1.
Ribeiro A, Riziotis I, Tyzack J, Borkakoti N, Thornton J
Nat Methods
. 2023 Sep;
20(10):1516-1522.
PMID: 37735566
Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation...
2.
Ribeiro A, Riziotis I, Tyzack J, Borkakoti N, Thornton J
Biophys Rev
. 2023 Jan;
14(6):1273-1280.
PMID: 36659981
Supplementary Information: The online version contains supplementary material available at 10.1007/s12551-022-01022-9.
3.
Noby N, Johnson R, Tyzack J, Embaby A, Saeed H, Hussein A, et al.
Int J Mol Sci
. 2022 May;
23(9).
PMID: 35563094
Cold active esterases have gained great interest in several industries. The recently determined structure of a family IV cold active esterase (EstN7) from strain N1 was used to expand its...
4.
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs
Santana C, Izidoro S, C de Melo-Minardi R, Tyzack J, Ribeiro A, Pires D, et al.
Nucleic Acids Res
. 2022 May;
50(W1):W392-W397.
PMID: 35524575
Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization...
5.
Zaru R, Onwubiko J, Ribeiro A, Cochrane K, Tyzack J, Muthukrishnan V, et al.
FEBS J
. 2021 Aug;
289(19):5875-5890.
PMID: 34437766
Enzymes play essential roles in all life processes and are used extensively in the biomedical and biotechnological fields. However, enzyme-related information is spread across multiple resources making its retrieval time-consuming....
6.
Santana C, de A Silveira S, Moraes J, Izidoro S, C de Melo-Minardi R, Ribeiro A, et al.
Bioinformatics
. 2020 Dec;
36(Suppl_2):i726-i734.
PMID: 33381849
Motivation: The discovery of protein-ligand-binding sites is a major step for elucidating protein function and for investigating new functional roles. Detecting protein-ligand-binding sites experimentally is time-consuming and expensive. Thus, a...
7.
Ribeiro A, Tyzack J, Borkakoti N, Holliday G, Thornton J
J Biol Chem
. 2019 Dec;
295(2):314-324.
PMID: 31796628
The catalytic residues of an enzyme comprise the amino acids located in the active center responsible for accelerating the enzyme-catalyzed reaction. These residues lower the activation energy of reactions by...
8.
Ribeiro A, Tyzack J, Borkakoti N, Thornton J
FEBS J
. 2019 Nov;
287(19):4128-4140.
PMID: 31733177
Pseudoenzymes are proteins that are evolutionary related to enzymes but lack relevant catalytic activity. They are usually evolved from enzymatic ancestors that have lost their catalytic activities. The loss of...
9.
Tyzack J, Ribeiro A, Borkakoti N, Thornton J
ACS Synth Biol
. 2019 Oct;
8(11):2494-2506.
PMID: 31647630
Transform-MinER (Transforming Molecules in Enzyme Reactions) is a web application facilitating the exploration of chemical biosynthetic space, guiding the user toward promising start points for enzyme design projects or directed...
10.
Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack J, Thornton J, Velankar S
Bioinformatics
. 2019 Feb;
35(18):3510-3511.
PMID: 30759194
Motivation: Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains >67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims...