Computational Prediction of RNA-Binding Proteins and Binding Sites

RNA-binding residues prediction using structural features

(2015) Huizhu Ren et al.   BMC BIOINFORMATICS

An Overview of the Prediction of Protein DNA-Binding Sites

(2015) Jingna Si et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An iridium(iii)-based irreversible protein–protein interaction inhibitor of BRD4 as a potent anticancer agent

(2015) Hai-Jing Zhong et al.   Chemical Science

Computationally predicting protein-RNA interactions using only positive and unlabeled examples

(2015) Zhanzhan Cheng et al.   Journal of Bioinformatics and Computational Biology

Antagonizing STAT3 Dimerization with a Rhodium(III) Complex

(2014) Dik-Lung Ma et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Predicting protein–RNA interaction amino acids using random forest based on submodularity subset selection

(2014) Xiaoyong Pan et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

An oligonucleotide-based label-free luminescent switch-on probe for RNA detection utilizing a G-quadruplex-selective iridium(iii) complex

(2014) Dik-Lung Ma et al.   Nanoscale

Prediction of RNA Binding Residues: An Extensive Analysis Based on Structure and Function to Select the Best Predictor

(2014) R. Nagarajan et al.   PLoS One

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

RBRDetector: Improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies

(2014) Xiao-Xia Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

(2013) F. Agostini et al.   BIOINFORMATICS

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational modeling of protein–RNA complex structures

(2013) Irina Tuszynska et al.   METHODS

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

(2013) Huiying Zhao et al.   Molecular BioSystems

A Metal-Based Inhibitor of Tumor Necrosis Factor-α

(2012) Chung-Hang Leung et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2012) Rasna R Walia et al.   BMC BIOINFORMATICS

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

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

(2011) Irina Tuszynska et al.   BMC BIOINFORMATICS

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

MetaDBSite: a meta approach to improve protein DNA-binding sites prediction

(2011) Jingna Si et al.   BMC Systems Biology

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

Prediction of RNA-Binding Proteins by Voting Systems

(2011) C. R. Peng et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

Computational methods for prediction of protein–RNA interactions

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

Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction

(2011) Shandar Ahmad et al.   BMC STRUCTURAL BIOLOGY

Structure-Based Discovery of Natural-Product-like TNF-α Inhibitors

(2010) Daniel Shiu-Hin Chan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2010) Zhi-Ping Liu et al.   BIOINFORMATICS

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

(2010) Liangjiang Wang et al.   BMC Systems Biology

Struct-NB: predicting protein-RNA binding sites using structural features

(2010) Fadi Towfic et al.   International Journal of Data Mining and Bioinformatics

SVM based prediction of RNA-binding proteins using binding residues and evolutionary information

(2010) Manish Kumar et al.   JOURNAL OF MOLECULAR RECOGNITION

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

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

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

(2010) H. Zhao et al.   NUCLEIC ACIDS RESEARCH

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

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

PRIDB: a protein-RNA interface database

(2010) B. A. Lewis et al.   NUCLEIC ACIDS RESEARCH

Improve the Prediction of RNA-Binding Residues Using Structural Neighbours

(2010) Quan Li et al.   PROTEIN AND PEPTIDE LETTERS

Grass: A server for the graphical representation and analysis of structures

(2010) Murad Nayal et al.   PROTEIN SCIENCE

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

Exploiting structural and topological information to improve prediction of RNA-protein binding sites

(2009) Stefan R Maetschke et al.   BMC BIOINFORMATICS

Protein-protein docking dealing with the unknown

(2009) Irina S. Moreira et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting DNA- and RNA-binding proteins from sequences with kernel methods

(2009) Xiaojian Shao et al.   JOURNAL OF THEORETICAL BIOLOGY

TIM-Finder: A new method for identifying TIM-barrel proteins

(2009) Jing-Na Si et al.   BMC STRUCTURAL BIOLOGY

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

(2008) Y. Wang et al.   AMINO ACIDS

Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence

(2008) Kotb Abdelmohsen et al.   BIOLOGICAL CHEMISTRY

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

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

Posttranscriptional Regulation of the Breast Cancer Susceptibility Gene BRCA1 by the RNA Binding Protein HuR

(2008) J. M. Saunus et al.   CANCER RESEARCH

RISP: A web-based server for prediction of RNA-binding sites in proteins

(2008) Jing Tong et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry

(2008) Yao Chi Chen et al.   NUCLEIC ACIDS RESEARCH

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

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

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