The role of phase separation in RNA modification: Both cause and effect

Y Lu, L Gan, S Di, F Nie, H Shi, R Wang, F Yang… - International Journal of …, 2024 - Elsevier
Phase separation is a critical mechanism for partitioning cellular functions by specific
aggregation of biological macromolecules. Recent studies have found that phase separation …

Accurate and fast prediction of intrinsically disordered protein by multiple protein language models and ensemble learning

S Xu, A Onoda - Journal of Chemical Information and Modeling, 2023 - ACS Publications
Intrinsically disordered proteins (IDPs) play a vital role in various biological processes and
have attracted increasing attention in the past few decades. Predicting IDPs from the primary …

Design of functional intrinsically disordered proteins

A Garg, NS González-Foutel, MB Gielnik… - Protein Engineering …, 2024 - academic.oup.com
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a
highly disordered state. These intrinsically disordered proteins pose a unique challenge to …

DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA–disease associations and graph convolutional networks

T Bai, K Yan, B Liu - Briefings in Bioinformatics, 2023 - academic.oup.com
MicroRNAs (miRNAs) are human post-transcriptional regulators in humans, which are
involved in regulating various physiological processes by regulating the gene expression …

Identify essential genes based on clustering based synthetic minority oversampling technique

H Shi, C Wu, T Bai, J Chen, Y Li, H Wu - Computers in Biology and …, 2023 - Elsevier
Prediction of essential genes in a life organism is one of the central tasks in synthetic
biology. Computational predictors are desired because experimental data is often …

A functional map of the human intrinsically disordered proteome

I Pritišanac, TR Alderson, Đ Kolarić, T Zarin, S Xie… - bioRxiv, 2024 - biorxiv.org
Intrinsically disordered regions (IDRs) represent at least one-third of the human proteome
and defy the established structure-function paradigm. Because IDRs often have limited …

IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models

Y Pang, B Liu - PLOS Computational Biology, 2023 - journals.plos.org
Intrinsically disordered proteins (IDPs) and regions (IDRs) are a class of functionally
important proteins and regions that lack stable three-dimensional structures under the native …

[HTML][HTML] Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions

N Ruiz-Molina, J Parsons, EL Decker… - Computational and …, 2023 - Elsevier
Human complement is the first line of defence against invading pathogens and is involved in
tissue homeostasis. Complement-targeted therapies to treat several diseases caused by a …

DisoFLAG: accurate prediction of protein intrinsic disorder and its functions using graph-based interaction protein language model

Y Pang, B Liu - BMC biology, 2024 - Springer
Intrinsically disordered proteins and regions (IDPs/IDRs) are functionally important proteins
and regions that exist as highly dynamic conformations under natural physiological …

Assessment of Disordered Linker Predictions in the CAID2 Experiment

K Wang, G Hu, Z Wu, VN Uversky, L Kurgan - Biomolecules, 2024 - mdpi.com
Disordered linkers (DLs) are intrinsically disordered regions that facilitate movement
between adjacent functional regions/domains, contributing to many key cellular functions …