BioLiP2: an updated structure database for biologically relevant ligand–protein interactions
C Zhang, X Zhang, PL Freddolino… - Nucleic Acids …, 2024 - academic.oup.com
With the progress of structural biology, the Protein Data Bank (PDB) has witnessed rapid
accumulation of experimentally solved protein structures. Since many structures are …
accumulation of experimentally solved protein structures. Since many structures are …
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 …
NetGO 3.0: protein language model improves large-scale functional annotations
As one of the state-of-the-art automated function prediction (AFP) methods, NetGO 2.0
integrates multi-source information to improve the performance. However, it mainly utilizes …
integrates multi-source information to improve the performance. However, it mainly utilizes …
A comprehensive survey of deep learning techniques in protein function prediction
R Dhanuka, JP Singh, A Tripathi - IEEE/ACM Transactions on …, 2023 - ieeexplore.ieee.org
Protein function prediction is a major challenge in the field of bioinformatics which aims at
predicting the functions performed by a known protein. Many protein data forms like protein …
predicting the functions performed by a known protein. Many protein data forms like protein …
[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 …
Topological point cloud clustering
We present Topological Point Cloud Clustering (TPCC), a new method to cluster points in an
arbitrary point cloud based on their contribution to global topological features. TPCC …
arbitrary point cloud based on their contribution to global topological features. TPCC …
EnsembleFam: towards more accurate protein family prediction in the twilight zone
Background Current protein family modeling methods like profile Hidden Markov Model
(pHMM), k-mer based methods, and deep learning-based methods do not provide very …
(pHMM), k-mer based methods, and deep learning-based methods do not provide very …
TripletGO: integrating transcript expression profiles with protein homology inferences for gene function prediction
Gene Ontology (GO) has been widely used to annotate functions of genes and gene
products. Here, we proposed a new method, TripletGO, to deduce GO terms of protein …
products. Here, we proposed a new method, TripletGO, to deduce GO terms of protein …
Genome-wide identification and analysis of NAC transcription factor family in two diploid wild relatives of cultivated sweet potato uncovers potential NAC genes related …
H Yan, G Ma, JA Teixeira da Silva, L Qiu, J Xu… - Frontiers in …, 2021 - frontiersin.org
NAC (NAM, ATAF1/2, and CUC2) proteins play a pivotal role in modulating plant
development and offer protection against biotic and abiotic stresses. Until now, no …
development and offer protection against biotic and abiotic stresses. Until now, no …