Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins

L Kurgan, G Hu, K Wang, S Ghadermarzi, B Zhao… - Nature …, 2023 - nature.com
Intrinsic disorder is instrumental for a wide range of protein functions, and its analysis, using
computational predictions from primary structures, complements secondary and tertiary …

Computational prediction of disordered binding regions

S Basu, D Kihara, L Kurgan - Computational and Structural Biotechnology …, 2023 - Elsevier
One of the key features of intrinsically disordered regions (IDRs) is their ability to interact
with a broad range of partner molecules. Multiple types of interacting IDRs were identified …

DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction

S Basu, J Gsponer, L Kurgan - Nucleic Acids Research, 2023 - academic.oup.com
Intrinsic disorder in proteins is relatively abundant in nature and essential for a broad
spectrum of cellular functions. While disorder can be accurately predicted from protein …

Comparative evaluation of AlphaFold2 and disorder predictors for prediction of intrinsic disorder, disorder content and fully disordered proteins

B Zhao, S Ghadermarzi, L Kurgan - Computational and Structural …, 2023 - Elsevier
We expand studies of AlphaFold2 (AF2) in the context of intrinsic disorder prediction by
comparing it against a broad selection of 20 accurate, popular and recently released …

HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins

F Zhang, M Li, J Zhang, L Kurgan - Nucleic Acids Research, 2023 - academic.oup.com
The sequence-based predictors of RNA-binding residues (RBRs) are trained on either
structure-annotated or disorder-annotated binding regions. A recent study of predictors of …

[HTML][HTML] Compositional bias of intrinsically disordered proteins and regions and their predictions

B Zhao, L Kurgan - Biomolecules, 2022 - mdpi.com
Intrinsically disordered regions (IDRs) carry out many cellular functions and vary in length
and placement in protein sequences. This diversity leads to variations in the underlying …

Identification of the RSX interactome in a marsupial shows functional coherence with the **st interactome during X inactivation

KL McIntyre, SA Waters, L Zhong, G Hart-Smith… - Genome biology, 2024 - Springer
The marsupial specific RSX lncRNA is the functional analogue of the eutherian specific
XIST, which coordinates X chromosome inactivation. We characterized the RSX interactome …

Resources for computational prediction of intrinsic disorder in proteins

L Kurgan - Methods, 2022 - Elsevier
With over 40 years of research, researchers in the intrinsic disorder prediction field
developed over 100 computational predictors. This review offers a holistic perspective of this …

An atlas of posttranslational modifications on RNA binding proteins

WE England, J Wang, S Chen, P Baldi… - Nucleic acids …, 2022 - academic.oup.com
RNA structure and function are intimately tied to RNA binding protein recognition and
regulation. Posttranslational modifications are chemical modifications which can control …

CLIP: accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information

Z Peng, Z Li, Q Meng, B Zhao… - Briefings in …, 2023 - academic.oup.com
One of key features of intrinsically disordered regions (IDRs) is facilitation of protein–protein
and protein–nucleic acids interactions. These disordered binding regions include molecular …