Two predicted α-helices within the prion-like domain of TIAR-1 play a crucial role in its association with stress granules in Caenorhabditis elegans

DA Fuentes-Jiménez, LS Salinas… - Frontiers in Cell and …, 2023 - frontiersin.org
Stress granules (SGs) are sites for mRNA storage, protection, and translation repression.
TIA1 and TIAR1 are two RNA-binding proteins that are key players in SGs formation in …

Full-length de novo protein structure determination from cryo-EM maps using deep learning

J He, SY Huang - Bioinformatics, 2021 - academic.oup.com
Motivation Advances in microscopy instruments and image processing algorithms have led
to an increasing number of Cryo-electron microscopy (cryo-EM) maps. However, building …

EvoStruct-Sub: An accurate Gram-positive protein subcellular localization predictor using evolutionary and structural features

MR Uddin, A Sharma, DM Farid, MM Rahman… - Journal of theoretical …, 2018 - Elsevier
Determining subcellular localization of proteins is considered as an important step towards
understanding their functions. Previous studies have mainly focused solely on Gene …

Overview update: computational prediction of intrinsic disorder in proteins

VN Uversky, L Kurgan - Current Protocols, 2023 - Wiley Online Library
There are over 100 computational predictors of intrinsic disorder. These methods predict
amino acid‐level propensities for disorder directly from protein sequences. The propensities …

[HTML][HTML] Applications of contact predictions to structural biology

F Simkovic, S Ovchinnikov, D Baker, DJ Rigden - IUCrJ, 2017 - scripts.iucr.org
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are
important for protein structure or function can lead to covariance between the two positions …

CapiPy: python-based GUI-application to assist in protein immobilization

D Roura Padrosa, V Marchini, F Paradisi - Bioinformatics, 2021 - academic.oup.com
Protein immobilization, while widespread to unlock enzyme potential in biocatalysis,
remains tied to a trial an error approach. Nonetheless, several databases and computational …

Engineered Salivary Peptides Reduce Enamel Demineralization Provoked by Cariogenic S. mutans Biofilm

LM Marin, Y Xiao, JA Cury, WL Siqueira - Microorganisms, 2022 - mdpi.com
Engineering of the acquired enamel pellicle using salivary peptides has been shown to be a
promising anticaries strategy. However, the mechanisms by which these peptides protect …

Protein fold recognition using HMM–HMM alignment and dynamic programming

J Lyons, KK Paliwal, A Dehzangi, R Heffernan… - Journal of theoretical …, 2016 - Elsevier
Detecting three dimensional structures of protein sequences is a challenging task in
biological sciences. For this purpose, protein fold recognition has been utilized as an …

Improved species-specific lysine acetylation site prediction based on a large variety of features set

Q Wuyun, W Zheng, Y Zhang, J Ruan, G Hu - PloS one, 2016 - journals.plos.org
Lysine acetylation is a major post-translational modification. It plays a vital role in numerous
essential biological processes, such as gene expression and metabolism, and is related to …

HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues

A Sharma, A Lysenko, Y López, A Dehzangi, R Sharma… - BMC genomics, 2019 - Springer
Background Post-translational modifications are viewed as an important mechanism for
controlling protein function and are believed to be involved in multiple important diseases …