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 …
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 …
[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 …
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery
The type IV bacterial secretion system (SS) is reported to be one of the most ubiquitous SSs
in nature and can induce serious conditions by secreting type IV SS effectors (T4SEs) into …
in nature and can induce serious conditions by secreting type IV SS effectors (T4SEs) into …
Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection
NQK Le, W Li, Y Cao - Briefings in Bioinformatics, 2023 - academic.oup.com
Protein crystallization is crucial for biology, but the steps involved are complex and
demanding in terms of external factors and internal structure. To save on experimental costs …
demanding in terms of external factors and internal structure. To save on experimental costs …
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles
Evolutionary information in the form of a Position-Specific Scoring Matrix (PSSM) is a widely
used and highly informative representation of protein sequences. Accordingly, PSSM-based …
used and highly informative representation of protein sequences. Accordingly, PSSM-based …
Functional advantages of conserved intrinsic disorder in RNA-binding proteins
M Varadi, F Zsolyomi, M Guharoy, P Tompa - PloS one, 2015 - journals.plos.org
Proteins form large macromolecular assemblies with RNA that govern essential molecular
processes. RNA-binding proteins have often been associated with conformational flexibility …
processes. RNA-binding proteins have often been associated with conformational flexibility …
Prediction of protein–RNA binding sites by a random forest method with combined features
Motivation: Protein–RNA interactions play a key role in a number of biological processes,
such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and …
such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and …
RBPPred: predicting RNA-binding proteins from sequence using SVM
X Zhang, S Liu - Bioinformatics, 2017 - academic.oup.com
Motivation Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding
proteins play critical roles in post-transcriptional regulation and have diverse roles in various …
proteins play critical roles in post-transcriptional regulation and have diverse roles in various …
A comprehensive comparative review of sequence-based predictors of DNA-and RNA-binding residues
Motivated by the pressing need to characterize protein–DNA and protein–RNA interactions
on large scale, we review a comprehensive set of 30 computational methods for high …
on large scale, we review a comprehensive set of 30 computational methods for high …