Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Naïve Bayes

An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis

(2013) Chuanxin Zou et al.   BMC BIOINFORMATICS

DomHR: Accurately Identifying Domain Boundaries in Proteins Using a Hinge Region Strategy

(2013) Xiao-yan Zhang et al.   PLoS One

Smoothness without Smoothing: Why Gaussian Naive Bayes Is Not Naive for Multi-Subject Searchlight Studies

(2013) Rajeev D. S. Raizada et al.   PLoS One

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt et al.   BIOINFORMATICS

Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search

(2012) Andrea Szabóová 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

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?

(2012) W. G. Touw et al.   BRIEFINGS IN BIOINFORMATICS

Atomistic modeling of protein–DNA interaction specificity: progress and applications

(2012) Limin Angela Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

DNA-Prot: Identification of DNA Binding Proteins from Protein Sequence Information using Random Forest

(2012) K. Krishna. Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

(2012) Tuo Zhang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters

(2012) Sucharita Dey et al.   NUCLEIC ACIDS RESEARCH

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

(2011) Hui-Lin Huang et al.   BMC BIOINFORMATICS

Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations

(2011) A.-L. Boulesteix 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

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

iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

(2011) Wei-Zhong Lin et al.   PLoS One

Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

(2011) Weiqiang Zhou et al.   Proteome Science

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

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility

(2010) Hua Zhang et al.   AMINO ACIDS

iDBPs: a web server for the identification of DNA binding proteins

(2010) Guy Nimrod et al.   BIOINFORMATICS

DROP: an SVM domain linker predictor trained with optimal features selected by random forest

(2010) Teppei Ebina et al.   BIOINFORMATICS

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites

(2010) Yoichi Murakami et al.   BIOINFORMATICS

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

(2010) H. Zhao et al.   BIOINFORMATICS

The Text-mining based PubChem Bioassay neighboring analysis

(2010) Lianyi Han et al.   BMC BIOINFORMATICS

Boosting the prediction and understanding of DNA-binding domains from sequence

(2010) R. E. Langlois 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

A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation

(2009) Qiwen Dong et al.   BIOINFORMATICS

Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features

(2009) Guy Nimrod et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

NNcon: improved protein contact map prediction using 2D-recursive neural networks

(2009) A. N. Tegge et al.   NUCLEIC ACIDS RESEARCH

A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome

(2009) Mu Gao et al.   PLoS Computational Biology

An ensemble of reduced alphabets with protein encoding based on grouped weight for predicting DNA-binding proteins

(2008) Loris Nanni et al.   AMINO ACIDS

Combing ontologies and dipeptide composition for predicting DNA-binding proteins

(2008) Loris Nanni et al.   AMINO ACIDS

Accurate sequence-based prediction of catalytic residues

(2008) Tuo Zhang et al.   BIOINFORMATICS

ROC analysis: applications to the classification of biological sequences and 3D structures

(2008) P. Sonego et al.   BRIEFINGS IN BIOINFORMATICS

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

(2008) Mu Gao et al.   NUCLEIC ACIDS RESEARCH

Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

(2008) Yanzhi Guo et al.   NUCLEIC ACIDS RESEARCH

Classifying RNA-Binding Proteins Based on Electrostatic Properties

(2008) Shula Shazman et al.   PLoS Computational Biology