[HTML][HTML] Evaluating native-like structures of RNA-protein complexes through the deep learning method

C Zeng, Y Jian, S Vosoughi, C Zeng, Y Zhao - Nature Communications, 2023 - nature.com
RNA-protein complexes underlie numerous cellular processes, including basic translation
and gene regulation. The high-resolution structure determination of the RNA-protein …

Recent methodology progress of deep learning for RNA–protein interaction prediction

X Pan, Y Yang, CQ Xia, AH Mirza… - Wiley Interdisciplinary …, 2019 - Wiley Online Library
Interactions between RNAs and proteins play essential roles in many important biological
processes. Benefitting from the advances of next generation sequencing technologies …

Accurate prediction of nucleic acid and protein-nucleic acid complexes using RoseTTAFoldNA

M Baek, R McHugh, I Anishchenko, D Baker, F DiMaio - bioRxiv, 2022 - biorxiv.org
Protein-nucleic acid complexes play critical roles in biology. Despite considerable recent
advances in protein structure prediction, the prediction of the structures of protein-nucleic …

[HTML][HTML] RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites

J Luo, L Liu, S Venkateswaran, Q Song, X Zhou - Scientific reports, 2017 - nature.com
RNA and protein interactions play crucial roles in multiple biological processes, while these
interactions are significantly influenced by the structures and sequences of protein and RNA …

A nonredundant structure dataset for benchmarking protein‐RNA computational docking

SY Huang, X Zou - Journal of computational chemistry, 2013 - Wiley Online Library
Protein–RNA interactions play an important role in many biological processes. The ability to
predict the molecular structures of protein–RNA complexes from docking would be valuable …

Prediction of RNA binding proteins comes of age from low resolution to high resolution

H Zhao, Y Yang, Y Zhou - Molecular BioSystems, 2013 - pubs.rsc.org
Networks of protein–RNA interactions is likely to be larger than protein–protein and protein–
DNA interaction networks because RNA transcripts are encoded tens of times more than …

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] HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence

W Jin, KW Brannan, K Kapeli, SS Park, HQ Tan… - Molecular Cell, 2023 - cell.com
RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and,
when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict …

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

H Zhao, Y Yang, Y Zhou - Nucleic acids research, 2011 - academic.oup.com
Mechanistic understanding of many key cellular processes often involves identification of
RNA binding proteins (RBPs) and RNA binding sites in two separate steps. Here, they are …

[HTML][HTML] Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

M Baek, R McHugh, I Anishchenko, H Jiang, D Baker… - Nature …, 2024 - nature.com
Protein–RNA and protein–DNA complexes play critical roles in biology. Despite
considerable recent advances in protein structure prediction, the prediction of the structures …