Protein representations: Encoding biological information for machine learning in biocatalysis

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F24%3A00081679" target="_blank" >RIV/00159816:_____/24:00081679 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14310/24:00138463

Výsledek na webu

<a href="https://www.sciencedirect.com/science/article/pii/S0734975024001538?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S0734975024001538?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.biotechadv.2024.108459" target="_blank" >10.1016/j.biotechadv.2024.108459</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Protein representations: Encoding biological information for machine learning in biocatalysis

Popis výsledku v původním jazyce

Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address this issue, the power of machine learning can be harnessed to produce predictive models that enable the in silico study and engineering of improved enzymatic properties. Such machine learning models, however, require the conversion of the complex biological information to a numerical input, also called protein representations. These inputs demand special attention to ensure the training of accurate and precise models, and, in this review, we therefore examine the critical step of encoding protein information to numeric representations for use in machine learning. We selected the most important approaches for encoding the three distinct biological protein representations - primary sequence, 3D structure, and dynamics - to explore their requirements for employment and inductive biases. Combined representations of proteins and substrates are also introduced as emergent tools in biocatalysis. We propose the division of fixed representations, a collection of rule-based encoding strategies, and learned representations extracted from the latent spaces of large neural networks. To select the most suitable protein representation, we propose two main factors to consider. The first one is the model setup, which is influenced by the size of the training dataset and the choice of architecture. The second factor is the model objectives such as consideration about the assayed property, the difference between wild-type models and mutant predictors, and requirements for explainability. This review is aimed at serving as a source of information and guidance for properly representing enzymes in future machine learning models for biocatalysis.

Název v anglickém jazyce

Protein representations: Encoding biological information for machine learning in biocatalysis

Popis výsledku anglicky

Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address this issue, the power of machine learning can be harnessed to produce predictive models that enable the in silico study and engineering of improved enzymatic properties. Such machine learning models, however, require the conversion of the complex biological information to a numerical input, also called protein representations. These inputs demand special attention to ensure the training of accurate and precise models, and, in this review, we therefore examine the critical step of encoding protein information to numeric representations for use in machine learning. We selected the most important approaches for encoding the three distinct biological protein representations - primary sequence, 3D structure, and dynamics - to explore their requirements for employment and inductive biases. Combined representations of proteins and substrates are also introduced as emergent tools in biocatalysis. We propose the division of fixed representations, a collection of rule-based encoding strategies, and learned representations extracted from the latent spaces of large neural networks. To select the most suitable protein representation, we propose two main factors to consider. The first one is the model setup, which is influenced by the size of the training dataset and the choice of architecture. The second factor is the model objectives such as consideration about the assayed property, the difference between wild-type models and mutant predictors, and requirements for explainability. This review is aimed at serving as a source of information and guidance for properly representing enzymes in future machine learning models for biocatalysis.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

30400 - Medical biotechnology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Biotechnology Advances

ISSN

0734-9750

e-ISSN

1873-1899

Svazek periodika

77

Číslo periodika v rámci svazku

October

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

20

Strana od-do

108459

Kód UT WoS článku

001332287000001

EID výsledku v databázi Scopus

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