Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

Phase Separation and Disorder-to-Order Transition of Human Brain Expressed X–Linked 3 (hBEX3) in the Presence of Small Fragments of tRNA

(2020) Mariana J. do Amaral et al.   JOURNAL OF MOLECULAR BIOLOGY

Japanese Encephalitis Virus: Exploring the dark proteome and disorder‐function paradigm

(2020) Taniya Bhardwaj et al.   FEBS Journal

SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences

(2019) Jian Zhang et al.   BIOINFORMATICS

Interactome of the Autoimmune Risk Protein ANKRD55

(2019) Nerea Ugidos et al.   Frontiers in Immunology

DISOselect: Disorder predictor selection at the protein level

(2019) Akila Katuwawala et al.   PROTEIN SCIENCE

DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server

(2019) Amita Barik et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks

(2018) Xiaoyong Pan et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

In Silico Prediction and Validation of Novel RNA Binding Proteins and Residues in the Human Proteome

(2018) Shomeek Chowdhury et al.   PROTEOMICS

Comprehensive Genomic Characterization of RNA-Binding Proteins across Human Cancers

(2018) Ze-Lin Wang et al.   Cell Reports

Improving the prediction of protein–nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods

(2018) Hong Su et al.   BIOINFORMATICS

Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

(2018) Chandran Nithin et al.   Genes

Quality assessment for the putative intrinsic disorder in proteins

(2018) Gang Hu et al.   BIOINFORMATICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

RNAcentral: a hub of information for non-coding RNA sequences

(2018) et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Partner‐specific Prediction of RNA‐binding Residues in Proteins: A Critical Assessment

(2018) Yong Jung et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach

(2017) Priyadarshini P. Pai et al.   JOURNAL OF THEORETICAL BIOLOGY

DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues

(2017) Jing Yan et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNAs and RNA-Binding Proteins in Oxidative Stress, Cellular Senescence, and Age-Related Diseases

(2017) Chongtae Kim et al.   Oxidative Medicine and Cellular Longevity

DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences

(2016) Fanchi Meng et al.   BIOINFORMATICS

PRIdictor: Protein–RNA Interaction predictor

(2016) Narankhuu Tuvshinjargal et al.   BIOSYSTEMS

Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors

(2016) Meijian Sun et al.   BMC BIOINFORMATICS

A structural perspective of RNA recognition by intrinsically disordered proteins

(2016) Sushmita Basu et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure

(2016) Chris A. Kieslich et al.   Journal of Chemical Information and Modeling

Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea

(2016) Chen Wang et al.   PROTEOMICS

RNA-binding proteins implicated in neurodegenerative diseases

(2016) Mark R Cookson   Wiley Interdisciplinary Reviews-RNA

Advances in the characterization of RNA-binding proteins

(2016) Domenica Marchese et al.   Wiley Interdisciplinary Reviews-RNA

FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues

(2016) Yasser EL-Manzalawy et al.   PLoS One

A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues

(2015) Jing Yan et al.   BRIEFINGS IN BIOINFORMATICS

In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces

(2015) Zhonghua Wu et al.   FEBS LETTERS

Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides

(2015) Bharat Panwar et al.   GENOMICS

SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues

(2015) Xiaoxia Yang et al.   PLoS One

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

(2015) Zhichao Miao et al.   PLoS Computational Biology

Quantifying sequence and structural features of protein–RNA interactions

(2014) Songling Li et al.   NUCLEIC ACIDS RESEARCH

RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins

(2014) Rasna R. Walia et al.   PLoS One

Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets

(2013) Sungwook Choi et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Comprehensively designed consensus of standalone secondary structure predictors improvesQ3by over 3%

(2013) Jing Yan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus

(2013) Xiao Fan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

(2013) Huiying Zhao et al.   Molecular BioSystems

The Nucleic Acid Database: new features and capabilities

(2013) Buvaneswari Coimbatore Narayanan et al.   NUCLEIC ACIDS RESEARCH

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

(2012) Lukasz P Kozlowski et al.   BMC BIOINFORMATICS

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

(2012) Rasna R Walia et al.   BMC BIOINFORMATICS

Comprehensive Comparative Assessment of In-Silico Predictors of Disordered Regions

(2012) Zhen-Ling Peng et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

Prediction of RNA-binding amino acids from protein and RNA sequences

(2011) Sungwook Choi et al.   BMC BIOINFORMATICS

Prediction of dinucleotide-specific RNA-binding sites in proteins

(2011) Michael Fernandez et al.   BMC BIOINFORMATICS

Critical assessment of high-throughput standalone methods for secondary structure prediction

(2011) H. Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Analysis and Prediction of RNA-Binding Residues Using Sequence, Evolutionary Conservation, and Predicted Secondary Structure and Solvent Accessibility

(2011) Tuo Zhang et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Computational methods for prediction of protein–RNA interactions

(2011) Tomasz Puton et al.   JOURNAL OF STRUCTURAL BIOLOGY

Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

(2011) Huiying Zhao et al.   RNA Biology

Identification of RNA-binding sites in proteins by integrating various sequence information

(2010) Cui-cui Wang et al.   AMINO ACIDS

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

(2010) Bin Xue et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Prediction of protein–RNA binding sites by a random forest method with combined features

(2010) Zhi-Ping Liu et al.   BIOINFORMATICS

Predicting RNA-binding residues from evolutionary information and sequence conservation

(2010) Yu-Feng Huang et al.   BMC GENOMICS

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

(2010) Liangjiang Wang et al.   BMC Systems Biology

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences

(2010) Y. Murakami et al.   NUCLEIC ACIDS RESEARCH

NAPS: a residue-level nucleic acid-binding prediction server

(2010) Matthew B. Carson et al.   NUCLEIC ACIDS RESEARCH

Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature

(2010) Xin Ma et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PRINTR: Prediction of RNA binding sites in proteins using SVM and profiles

(2008) Y. Wang et al.   AMINO ACIDS

Predicting RNA-binding sites of proteins using support vector machines and evolutionary information

(2008) Cheng-Wei Cheng et al.   BMC BIOINFORMATICS

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Prediction of RNA binding sites in a protein using SVM and PSSM profile

(2007) Manish Kumar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS