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

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

(2012) Rasna R Walia et al.   BMC BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

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

(2011) Irina Tuszynska et al.   BMC 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

Prediction of RNA-Binding Proteins by Voting Systems

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

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

(2011) Eshel Faraggi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational methods for prediction of protein–RNA interactions

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

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

A coarse-grained force field for Protein–RNA docking

(2011) Piotr Setny et al.   NUCLEIC ACIDS RESEARCH

Efficient detection of RNA-protein interactions using tethered RNAs

(2011) H. Iioka et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Shandar Ahmad et al.   BMC STRUCTURAL BIOLOGY

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

Annotating non-coding regions of the genome

(2010) Roger P. Alexander et al.   NATURE REVIEWS GENETICS

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

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

(2010) Nikoleta G. Tsvetanova et al.   PLoS One

A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

(2010) Tanja Scherrer et al.   PLoS One

Improve the Prediction of RNA-Binding Residues Using Structural Neighbours

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

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue; identification of potential players in tumor formation

(2010) Pedro A. F. Galante et al.   RNA Biology

Protein function annotation from sequence: prediction of residues interacting with RNA

(2009) R. V. Spriggs et al.   BIOINFORMATICS

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

(2009) Stefan R Maetschke et al.   BMC BIOINFORMATICS

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

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

Exploration of Uncharted Regions of the Protein Universe

(2009) Lukasz Jaroszewski et al.   PLOS BIOLOGY

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

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

RNA recognition motifs: boring? Not quite

(2008) Antoine Cléry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

(2008) A. Shulman-Peleg et al.   NUCLEIC ACIDS RESEARCH

Local Function Conservation in Sequence and Structure Space

(2008) Nils Weinhold et al.   PLoS Computational Biology

Classifying RNA-Binding Proteins Based on Electrostatic Properties

(2008) Shula Shazman et al.   PLoS Computational Biology

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

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

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE