Machine learning in enzyme engineering

S Mazurenko, Z Prokop, J Damborsky - ACS catalysis, 2019 - ACS Publications
Enzyme engineering plays a central role in develo** efficient biocatalysts for
biotechnology, biomedicine, and life sciences. Apart from classical rational design and …

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

FB Bastian, J Roux, A Niknejad, A Comte… - Nucleic acids …, 2021 - academic.oup.com
Bgee is a database to retrieve and compare gene expression patterns in multiple animal
species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ …

[PDF][PDF] Gene ontology: pitfalls, biases, and remedies

P Gaudet, C Dessimoz - The gene ontology handbook, 2017 - library.oapen.org
Abstract The Gene Ontology (GO) is a formidable resource, but there are several
considerations about it that are essential to understand the data and interpret it correctly …

Propagation, detection and correction of errors using the sequence database network

B Goudey, N Geard, K Verspoor… - Briefings in …, 2022 - academic.oup.com
Nucleotide and protein sequences stored in public databases are the cornerstone of many
bioinformatics analyses. The records containing these sequences are prone to a wide range …

ECO, the Evidence & Conclusion Ontology: community standard for evidence information

M Giglio, R Tauber, S Nadendla, J Munro… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Evidence and Conclusion Ontology (ECO) contains terms (classes) that
describe types of evidence and assertion methods. ECO terms are used in the process of …

Machine learning enables prediction of pyrrolysyl-tRNA synthetase substrate specificity

Q Zhang, W Zheng, Z Song, Q Zhang, L Yang… - ACS Synthetic …, 2023 - ACS Publications
Knowledge about the substrate scope for a given enzyme is informative for elucidating
biochemical pathways and also for expanding applications of the enzyme. However, no …

Homology modeling in drug discovery-an update on the last decade

G Munsamy, MES Soliman - Letters in Drug Design & Discovery, 2017 - benthamdirect.com
Background: The continual evolution of the world is closely chaperoned by the emergence
of deadly diseases, which presents itself at every turn thus determining the 3D structure of a …

Functional annotations of paralogs: a blessing and a curse

R Zallot, KJ Harrison, B Kolaczkowski… - Life, 2016 - mdpi.com
Gene duplication followed by mutation is a classic mechanism of neofunctionalization,
producing gene families with functional diversity. In some cases, a single point mutation is …

Molecular interaction studies of Deguelin and its derivatives with Cyclin D1 and Cyclin E in cancer cell signaling pathway: The computational approach

KB Lokhande, S Nagar, KV Swamy - Scientific reports, 2019 - nature.com
Deguelin is a major active ingredient and principal component in several plants and it is a
potential molecule to target proteins of cancer cell signaling pathway. As a complex natural …

Transcriptome signatures in the brain of a migratory songbird

RC Frias-Soler, LV Pildaín, LG Pârâu, M Wink… - … and Physiology Part D …, 2020 - Elsevier
Most of the birds's adaptations for migration have a neuroendocrine origin, triggered by
changes in photoperiod and the patterns of Earth's magnetic field. Migration …