DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches

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

DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry

(2012) Yao Chi Chen et al.   NUCLEIC ACIDS RESEARCH

Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement

(2012) Ambrish Roy et al.   STRUCTURE

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 Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network

(2011) Rong Liu et al.   PLoS One

Assessment of ligand-binding residue predictions in CASP9

(2011) Tobias Schmidt et al.   PROTEINS-STRUCTURE FUNCTION AND 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

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

(2010) Liangjiang Wang et al.   BMC Systems Biology

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

(2010) Pemra Ozbek et al.   NUCLEIC ACIDS RESEARCH

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

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

Protein interface conservation across structure space

(2010) Q. C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An accurate feature-based method for identifying DNA-binding residues on protein surfaces

(2010) Yi Xiong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator

(2008) Colin Levy et al.   MOLECULAR MICROBIOLOGY

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

(2008) Mu Gao et al.   NUCLEIC ACIDS RESEARCH

Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

(2008) Shandar Ahmad et al.   NUCLEIC ACIDS RESEARCH

PSAIA - Protein Structure and Interaction Analyzer

(2008) Josip Mihel et al.   BMC STRUCTURAL BIOLOGY