Specificity and nonspecificity in RNA–protein interactions
E Jankowsky, ME Harris - Nature reviews Molecular cell biology, 2015 - nature.com
To fully understand the regulation of gene expression, it is critical to quantitatively define
whether and how RNA-binding proteins (RBPs) discriminate between alternative binding …
whether and how RNA-binding proteins (RBPs) discriminate between alternative binding …
Comprehensive review and empirical analysis of hallmarks of DNA-, RNA-and protein-binding residues in protein chains
Proteins interact with a variety of molecules including proteins and nucleic acids. We review
a comprehensive collection of over 50 studies that analyze and/or predict these interactions …
a comprehensive collection of over 50 studies that analyze and/or predict these interactions …
[PDF][PDF] DRNApred, fast sequence-based method that accurately predicts and discriminates DNA-and RNA-binding residues
J Yan, L Kurgan - Nucleic acids research, 2017 - academic.oup.com
Protein-DNA and protein-RNA interactions are part of many diverse and essential cellular
functions and yet most of them remain to be discovered and characterized. Recent research …
functions and yet most of them remain to be discovered and characterized. Recent research …
High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder
Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under
physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with …
physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with …
[HTML][HTML] A deep learning framework for robust and accurate prediction of ncRNA-protein interactions using evolutionary information
The interactions between non-coding RNAs (ncRNAs) and proteins play an important role in
many biological processes, and their biological functions are primarily achieved by binding …
many biological processes, and their biological functions are primarily achieved by binding …
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 …
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins
Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control
of gene expression, including splicing, transport, polyadenylation and RNA stability. To …
of gene expression, including splicing, transport, polyadenylation and RNA stability. To …
RNA–protein interactions: an overview
RNA binding proteins (RBPs) are key players in the regulation of gene expression. In this
chapter we discuss the main protein–RNA recognition modes used by RBPs in order to …
chapter we discuss the main protein–RNA recognition modes used by RBPs in order to …
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 …
Review and comparative assessment of sequence-based predictors of protein-binding residues
Understanding of molecular mechanisms that govern protein–protein interactions and
accurate modeling of protein–protein docking rely on accurate identification and prediction …
accurate modeling of protein–protein docking rely on accurate identification and prediction …