Protein–RNA interaction prediction with deep learning: structure matters
Protein–RNA interactions are of vital importance to a variety of cellular activities. Both
experimental and computational techniques have been developed to study the interactions …
experimental and computational techniques have been developed to study the interactions …
In silico molecular docking in DNA aptamer development
Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that
exhibit binding affinity and specificity against a wide variety of target molecules. Compared …
exhibit binding affinity and specificity against a wide variety of target molecules. Compared …
[HTML][HTML] Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet
RNA-binding proteins play crucial roles in the regulation of gene expression, and
understanding the interactions between RNAs and RBPs in distinct cellular conditions forms …
understanding the interactions between RNAs and RBPs in distinct cellular conditions forms …
Transcriptome-wide discovery of coding and noncoding RNA-binding proteins
Transcriptome-wide identification of RNA-binding proteins (RBPs) is a prerequisite for
understanding the posttranscriptional gene regulation networks. However, proteomic …
understanding the posttranscriptional gene regulation networks. However, proteomic …
[HTML][HTML] SONAR discovers RNA-binding proteins from analysis of large-scale protein-protein interactomes
RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding
proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to …
proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to …
ProNA2020 predicts protein–DNA, protein–RNA, and protein–protein binding proteins and residues from sequence
J Qiu, M Bernhofer, M Heinzinger, S Kemper… - Journal of molecular …, 2020 - Elsevier
The intricate details of how proteins bind to proteins, DNA, and RNA are crucial for the
understanding of almost all biological processes. Disease-causing sequence variants often …
understanding of almost all biological processes. Disease-causing sequence variants often …
DescribePROT: database of amino acid-level protein structure and function predictions
We present DescribePROT, the database of predicted amino acid-level descriptors of
structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 …
structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 …
Advances in the characterization of RNA‐binding proteins
D Marchese, NS de Groot… - Wiley …, 2016 - Wiley Online Library
From transcription, to transport, storage, and translation, RNA depends on association with
different RNA‐binding proteins (RBPs). Methods based on next‐generation sequencing and …
different RNA‐binding proteins (RBPs). Methods based on next‐generation sequencing and …
Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes
Molecular docking provides a computationally efficient way to predict the atomic structural
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …
regulation of the cancer epigenome by long non-coding RNAs
ME Forrest, AM Khalil - Cancer Letters, 2017 - Elsevier
Long non-coding RNAs have emerged as highly versatile players in the regulation of gene
expression in development and human disease, particularly cancer. Hundreds of lncRNAs …
expression in development and human disease, particularly cancer. Hundreds of lncRNAs …