flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

G Hu, A Katuwawala, K Wang, Z Wu… - Nature …, 2021 - nature.com
Identification of intrinsic disorder in proteins relies in large part on computational predictors,
which demands that their accuracy should be high. Since intrinsic disorder carries out a …

Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology

M Bertoni, F Kiefer, M Biasini, L Bordoli, T Schwede - Scientific reports, 2017 - nature.com
Cellular processes often depend on interactions between proteins and the formation of
macromolecular complexes. The impairment of such interactions can lead to deregulation of …

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

Z Peng, J Yan, X Fan, MJ Mizianty, B Xue… - Cellular and Molecular …, 2015 - Springer
Recent years witnessed increased interest in intrinsically disordered proteins and regions.
These proteins and regions are abundant and possess unique structural features and a …

UniRef: comprehensive and non-redundant UniProt reference clusters

BE Suzek, H Huang, P McGarvey, R Mazumder… - …, 2007 - academic.oup.com
Motivation: Redundant protein sequences in biological databases hinder sequence
similarity searches and make interpretation of search results difficult. Clustering of protein …

Predicting functionally important residues from sequence conservation

JA Capra, M Singh - Bioinformatics, 2007 - academic.oup.com
Motivation: All residues in a protein are not equally important. Some are essential for the
proper structure and function of the protein, whereas others can be readily replaced …

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

JA Capra, RA Laskowski, JM Thornton… - PLoS computational …, 2009 - journals.plos.org
Identifying a protein's functional sites is an important step towards characterizing its
molecular function. Numerous structure-and sequence-based methods have been …

[HTML][HTML] Geminiviral C4/AC4 proteins: An emerging component of the viral arsenal against plant defence

R Kumar, I Dasgupta - Virology, 2023 - Elsevier
Virus infection triggers a plethora of defence reactions in plants to incapacitate the intruder.
Viruses, in turn, have added additional functions to their genes so that they acquire …

Precise prediction of phase-separation key residues by machine learning

J Sun, J Qu, C Zhao, X Zhang, X Liu, J Wang… - Nature …, 2024 - nature.com
Understanding intracellular phase separation is crucial for deciphering transcriptional
control, cell fate transitions, and disease mechanisms. However, the key residues, which …

DescribePROT: database of amino acid-level protein structure and function predictions

B Zhao, A Katuwawala, CJ Oldfield… - Nucleic Acids …, 2021 - academic.oup.com
We present DescribePROT, the database of predicted amino acid-level descriptors of
structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 …

Prediction of protein-protein interaction sites in intrinsically disordered proteins

R Chen, X Li, Y Yang, X Song, C Wang… - Frontiers in Molecular …, 2022 - frontiersin.org
Intrinsically disordered proteins (IDPs) participate in many biological processes by
interacting with other proteins, including the regulation of transcription, translation, and the …