Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

Cross-validation under separate sampling: strong bias and how to correct it

(2014) Ulisses M. Braga-Neto et al.   BIOINFORMATICS

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

Quantifying sequence and structural features of protein–RNA interactions

(2014) Songling Li et al.   NUCLEIC ACIDS RESEARCH

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

'Oming in on RNA–protein interactions

(2014) John L Rinn et al.   GENOME BIOLOGY

PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information

(2013) Tao Li et al.   BIOINFORMATICS

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

(2013) Gershon Celniker et al.   ISRAEL JOURNAL OF CHEMISTRY

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

(2013) Huiying Zhao et al.   Molecular BioSystems

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Interactive Web-Based Pointillist Visualization of Hydrogenic Orbitals Using Jmol

(2012) Shane P. Tully et al.   JOURNAL OF CHEMICAL EDUCATION

A nonredundant structure dataset for benchmarking protein-RNA computational docking

(2012) Sheng-You Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

NPIDB: nucleic acid—protein interaction database

(2012) Dmitry D. Kirsanov et al.   NUCLEIC ACIDS RESEARCH

Computational methods for prediction of protein–RNA interactions

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

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

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

DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues

(2010) Pemra Ozbek et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy 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

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

Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins

(2009) Laura Pérez-Cano et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

(2009) Munazah Andrabi et al.   BMC STRUCTURAL BIOLOGY

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

(2008) Jiansheng Wu et al.   BIOINFORMATICS

A protein-DNA docking benchmark

(2008) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions

(2008) Mu Gao et al.   NUCLEIC ACIDS RESEARCH

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

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

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