Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence
Annotating protein sequences according to their biological functions is one of the key steps
in understanding microbial diversity, metabolic potentials, and evolutionary histories …
in understanding microbial diversity, metabolic potentials, and evolutionary histories …
A systematic review of state-of-the-art strategies for machine learning-based protein function prediction
TC Yan, ZX Yue, HQ Xu, YH Liu, YF Hong… - Computers in Biology …, 2023 - Elsevier
New drug discovery is inseparable from the discovery of drug targets, and the vast majority
of the known targets are proteins. At the same time, proteins are essential structural and …
of the known targets are proteins. At the same time, proteins are essential structural and …
TEMPROT: protein function annotation using transformers embeddings and homology search
Background Although the development of sequencing technologies has provided a large
number of protein sequences, the analysis of functions that each one plays is still difficult …
number of protein sequences, the analysis of functions that each one plays is still difficult …
Ten quick tips for sequence-based prediction of protein properties using machine learning
The ubiquitous availability of genome sequencing data explains the popularity of machine
learning-based methods for the prediction of protein properties from their amino acid …
learning-based methods for the prediction of protein properties from their amino acid …
Assessing the role of evolutionary information for enhancing protein language model embeddings
Abstract Embeddings from protein Language Models (pLMs) are replacing evolutionary
information from multiple sequence alignments (MSAs) as the most successful input for …
information from multiple sequence alignments (MSAs) as the most successful input for …
[HTML][HTML] Functional characterization of prokaryotic dark matter: the road so far and what lies ahead
P Escudeiro, CS Henry, RPM Dias - Current Research in Microbial …, 2022 - Elsevier
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer
than two-hundred thousand prokaryotic species have been described. This uncharted …
than two-hundred thousand prokaryotic species have been described. This uncharted …
[HTML][HTML] Heterogeneous network approaches to protein pathway prediction
Understanding protein-protein interactions (PPIs) and the pathways they comprise is
essential for comprehending cellular functions and their links to specific phenotypes …
essential for comprehending cellular functions and their links to specific phenotypes …
An exhaustive review of computational prediction techniques for PPI sites, protein locations, and protein functions
The field of proteomics encompasses a comprehensive examination of proteins,
encompassing their structural properties, interactions with other biomolecules, subcellular …
encompassing their structural properties, interactions with other biomolecules, subcellular …
[HTML][HTML] FunPredCATH: An ensemble method for predicting protein function using CATH
Motivation The growth of unannotated proteins in UniProt increases at a very high rate every
year due to more efficient sequencing methods. However, the experimental annotation of …
year due to more efficient sequencing methods. However, the experimental annotation of …
[HTML][HTML] Revelation of potent ES-62 activity of a hypothetical protein from Wuchereria bancrofti proteome by in-silico based characterization and functional annotation
Lymphatic filariasis (LF) is a well-known disease caused primarily by the parasitic worm
Wuchereria bancrofti, although other Filarioidea parasites, including Brugia malayi and …
Wuchereria bancrofti, although other Filarioidea parasites, including Brugia malayi and …