Interactions by disorder–a matter of context

K Bugge, I Brakti, CB Fernandes, JE Dreier… - Frontiers in Molecular …, 2020 - frontiersin.org
Living organisms depend on timely and organized interactions between proteins linked in
interactomes of high complexity. The recent increased precision by which protein …

Intrinsically disordered proteins play diverse roles in cell signaling

SE Bondos, AK Dunker, VN Uversky - Cell Communication and Signaling, 2022 - Springer
Signaling pathways allow cells to detect and respond to a wide variety of chemical (eg Ca2+
or chemokine proteins) and physical stimuli (eg, sheer stress, light). Together, these …

SPOT-Disorder2: improved protein intrinsic disorder prediction by ensembled deep learning

J Hanson, KK Paliwal, T Litfin… - Genomics, Proteomics …, 2019 - academic.oup.com
Intrinsically disordered or unstructured proteins (or regions in proteins) have been found to
be important in a wide range of biological functions and implicated in many diseases. Due to …

Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning

J Hanson, T Litfin, K Paliwal, Y Zhou - Bioinformatics, 2020 - academic.oup.com
Motivation Protein intrinsic disorder describes the tendency of sequence residues to not fold
into a rigid three-dimensional shape by themselves. However, some of these disordered …

[HTML][HTML] Computational prediction of MoRFs, short disorder-to-order transitioning protein binding regions

A Katuwawala, Z Peng, J Yang, L Kurgan - Computational and Structural …, 2019 - Elsevier
Molecular recognition features (MoRFs) are short protein-binding regions that undergo
disorder-to-order transitions (induced folding) upon binding protein partners. These regions …

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 …

Protein function analysis through machine learning

C Avery, J Patterson, T Grear, T Frater, DJ Jacobs - Biomolecules, 2022 - mdpi.com
Machine learning (ML) has been an important arsenal in computational biology used to
elucidate protein function for decades. With the recent burgeoning of novel ML methods and …

APOD: accurate sequence-based predictor of disordered flexible linkers

Z Peng, Q Xing, L Kurgan - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation Disordered flexible linkers (DFLs) are abundant and functionally
important intrinsically disordered regions that connect protein domains and structural …

Computational Prediction of Linear Interacting Peptides

N Malhis, J Gsponer - Prediction of Protein Secondary Structure, 2024 - Springer
Intrinsically disordered protein regions, IDRs, are observed in many eukaryotic proteins.
They play critical roles in essentially all cellular processes because segments of these …

DMFpred: predicting protein disorder molecular functions based on protein cubic language model

Y Pang, B Liu - PLOS Computational Biology, 2022 - journals.plos.org
Intrinsically disordered proteins and regions (IDP/IDRs) are widespread in living organisms
and perform various essential molecular functions. These functions are summarized as six …