Published in BMC Bioinformatics on February 19, 2005
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res (2006) 3.29
Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics (2006) 1.75
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res (2007) 1.68
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics (2008) 1.58
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol (2010) 1.53
Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network. BMC Struct Biol (2007) 1.45
Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. FEBS Lett (2007) 1.37
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information. BMC Bioinformatics (2006) 1.20
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol (2009) 1.19
NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Res (2010) 1.16
Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics (2009) 1.16
Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties. PLoS One (2010) 1.15
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinformatics (2012) 1.09
Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis. Plant Cell (2010) 1.06
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res (2008) 1.04
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. BMC Syst Biol (2011) 1.01
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. BMC Bioinformatics (2010) 1.00
Prediction of protein binding sites in protein structures using hidden Markov support vector machine. BMC Bioinformatics (2009) 0.98
TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences. PLoS One (2012) 0.95
Homology modeling of human Toll-like receptors TLR7, 8, and 9 ligand-binding domains. Protein Sci (2009) 0.94
Predicting residue-wise contact orders in proteins by support vector regression. BMC Bioinformatics (2006) 0.94
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. BMC Struct Biol (2009) 0.93
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. Nucleic Acids Res (2009) 0.93
DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res (2010) 0.92
Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics (2011) 0.91
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database (Oxford) (2013) 0.90
Exploiting a reduced set of weighted average features to improve prediction of DNA-binding residues from 3D structures. PLoS One (2011) 0.90
NestedMICA as an ab initio protein motif discovery tool. BMC Bioinformatics (2008) 0.89
Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score. Nucleic Acids Res (2015) 0.88
Prodepth: predict residue depth by support vector regression approach from protein sequences only. PLoS One (2009) 0.87
Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. Nucleic Acids Res (2012) 0.87
eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des (2013) 0.86
SySAP: a system-level predictor of deleterious single amino acid polymorphisms. Protein Cell (2011) 0.86
DBSI: DNA-binding site identifier. Nucleic Acids Res (2013) 0.85
Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res (2007) 0.85
A unified multitask architecture for predicting local protein properties. PLoS One (2012) 0.84
A graph kernel method for DNA-binding site prediction. BMC Syst Biol (2014) 0.84
PalmPred: an SVM based palmitoylation prediction method using sequence profile information. PLoS One (2014) 0.84
ParaDock: a flexible non-specific DNA--rigid protein docking algorithm. Nucleic Acids Res (2011) 0.84
Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC Biochem (2011) 0.84
LipocalinPred: a SVM-based method for prediction of lipocalins. BMC Bioinformatics (2009) 0.83
A survey of computational intelligence techniques in protein function prediction. Int J Proteomics (2014) 0.83
DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res (2012) 0.83
Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. Nucleic Acids Res (2013) 0.82
Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Res (2015) 0.82
svmPRAT: SVM-based protein residue annotation toolkit. BMC Bioinformatics (2009) 0.81
A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs. PLoS Comput Biol (2015) 0.81
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins. BMC Bioinformatics (2011) 0.81
Prediction and analysis of protein hydroxyproline and hydroxylysine. PLoS One (2010) 0.81
Predicting secretory proteins of malaria parasite by incorporating sequence evolution information into pseudo amino acid composition via grey system model. PLoS One (2012) 0.81
Structural models of protein-DNA complexes based on interface prediction and docking. Curr Protein Pept Sci (2011) 0.80
An overview of the prediction of protein DNA-binding sites. Int J Mol Sci (2015) 0.79
Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinformatics (2008) 0.79
Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome. PLoS One (2014) 0.79
Effective identification of Gram-negative bacterial type III secreted effectors using position-specific residue conservation profiles. PLoS One (2013) 0.79
Identification of DNA-binding proteins using support vector machine with sequence information. Comput Math Methods Med (2013) 0.79
DNA-binding residues and binding mode prediction with binding-mechanism concerned models. BMC Genomics (2009) 0.78
SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues. PLoS One (2015) 0.78
RNA-binding residues prediction using structural features. BMC Bioinformatics (2015) 0.78
SVM based model generation for binding site prediction on helix turn helix motif type of transcription factors in eukaryotes. Bioinformation (2013) 0.77
Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection. Biomed Res Int (2015) 0.77
Nucleotide excision repair in Trypanosoma brucei: specialization of transcription-coupled repair due to multigenic transcription. Mol Microbiol (2014) 0.76
Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties. Mol Genet Genomics (2014) 0.76
DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues. PLoS One (2016) 0.75
qiRNApredictor: A Novel Computational Program for the Prediction of qiRNAs in Neurospora crassa. PLoS One (2016) 0.75
PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context. Sci Rep (2016) 0.75
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PLoS One (2016) 0.75
On the Accuracy of Sequence-Based Computational Inference of Protein Residues Involved in Interactions with DNA. Trends Appl Sci Res (2008) 0.75
Predicting protein-binding regions in RNA using nucleotide profiles and compositions. BMC Syst Biol (2017) 0.75
An ensemble approach for large-scale identification of protein- protein interactions using the alignments of multiple sequences. Oncotarget (2016) 0.75
A novel method of predicting protein disordered regions based on sequence features. Biomed Res Int (2013) 0.75
An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA. BMC Genomics (2016) 0.75
Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers. J Comput Aided Mol Des (2016) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins (2000) 6.22
Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci U S A (1993) 3.92
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics (2004) 3.45
Accurate prediction of solvent accessibility using neural networks-based regression. Proteins (2004) 2.54
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol (2002) 2.52
Annotating nucleic acid-binding function based on protein structure. J Mol Biol (2003) 2.46
Protein sequence databases. Curr Opin Chem Biol (2004) 2.43
Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol (2000) 2.32
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Res (1998) 1.94
Moment-based prediction of DNA-binding proteins. J Mol Biol (2004) 1.79
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding. J Mol Biol (2002) 1.28
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics (2004) 3.45
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res (2006) 2.81
Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res (2011) 2.81
ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res (2004) 2.65
PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics (2009) 2.07
ASAView: database and tool for solvent accessibility representation in proteins. BMC Bioinformatics (2004) 1.94
Real value prediction of solvent accessibility from amino acid sequence. Proteins (2003) 1.86
Moment-based prediction of DNA-binding proteins. J Mol Biol (2004) 1.79
Classification of protein-DNA complexes based on structural descriptors. Structure (2006) 1.71
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J Mol Biol (2004) 1.69
ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0. Nucleic Acids Res (2002) 1.43
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. Bioinformatics (2003) 1.42
Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res (2007) 1.41
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding. J Mol Biol (2002) 1.28
The Diamond STING server. Nucleic Acids Res (2005) 1.18
Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition. J Am Chem Soc (2005) 1.18
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. BMC Bioinformatics (2007) 1.15
The role of alternative translation start sites in the generation of human protein diversity. Mol Genet Genomics (2005) 1.14
uORFs, reinitiation and alternative translation start sites in human mRNAs. FEBS Lett (2008) 1.07
Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations. Biopolymers (2002) 1.05
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res (2008) 1.04
Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry (2002) 1.03
Role of inter and intramolecular interactions in protein-DNA recognition. Gene (2005) 0.93
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. Nucleic Acids Res (2006) 0.93
Characterization of BRCAA1 and its novel antigen epitope identification. Cancer Epidemiol Biomarkers Prev (2004) 0.93
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks. BMC Struct Biol (2009) 0.93
Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif. Structure (2003) 0.92
Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics (2011) 0.91
Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. BMC Struct Biol (2011) 0.89
Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis. Biopolymers (2004) 0.88
A signature-based method for indexing cell cycle phase distribution from microarray profiles. BMC Genomics (2009) 0.86
Thermodynamic database for proteins: features and applications. Methods Mol Biol (2010) 0.86
Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). Mol Divers (2010) 0.85
CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Res (2010) 0.84
Contribution of a single hydrogen bond between betaHis81 of MHC class II I-E(k) and the bound peptide to the pH-dependent thermal stability. Microbiol Immunol (2004) 0.83
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. Nucleic Acids Res (2007) 0.82
NF-E2 p45 is important for establishing normal function of platelets. Mol Cell Biol (2013) 0.81
DeltaG-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome. FEBS J (2008) 0.81
Atom-wise statistics and prediction of solvent accessibility in proteins. Biophys Chem (2006) 0.81
A generalized conformational energy function of DNA derived from molecular dynamics simulations. Nucleic Acids Res (2009) 0.80
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins. Nucleic Acids Res (2004) 0.80
Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. Comput Biol Chem (2012) 0.80
Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803. FEBS Lett (2004) 0.80
A new method for evaluating the specificity of indirect readout in protein-DNA recognition. Nucleic Acids Res (2012) 0.79
Dimensionality of amino acid space and solvent accessibility prediction with neural networks. Comput Biol Chem (2006) 0.78
Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. Bioinformatics (2004) 0.78
Knowledge-based prediction of DNA atomic structure from nucleic sequence. Genome Inform (2005) 0.77
Proteochemometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines. J Chem Inf Model (2010) 0.77
Anatomy of specific interactions between lambda repressor and operator DNA. Proteins (2003) 0.77
Thermodynamic analysis of the increased stability of major histocompatibility complex class II molecule I-Ek complexed with an antigenic peptide at an acidic pH. J Biol Chem (2003) 0.77
Free energy calculations for the relative binding affinity between DNA and lambda-repressor. Proteins (2003) 0.77
MHC class II DR classification based on antigen-binding groove natural selection. Biochem Biophys Res Commun (2009) 0.77
Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast. Genome Inform (2009) 0.76
Bound peptide-dependent thermal stability of major histocompatibility complex class II molecule I-Ek. Biochemistry (2004) 0.75