Enabling full‐length evolutionary profiles based deep convolutional neural network for predicting DNA‐binding proteins from sequence

ECG anomaly class identification using LSTM and error profile modeling

(2019) Sucheta Chauhan et al.   COMPUTERS IN BIOLOGY AND MEDICINE

HFSP: high speed homology-driven function annotation of proteins

(2018) Yannick Mahlich et al.   BIOINFORMATICS

DBPPred-PDSD: Machine learning approach for prediction of DNA-binding proteins using Discrete Wavelet Transform and optimized integrated features space

(2018) Farman Ali et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Local-DPP: An improved DNA-binding protein prediction method by exploring local evolutionary information

(2017) Leyi Wei et al.   INFORMATION SCIENCES

PSFM-DBT: Identifying DNA-Binding Proteins by Combing Position Specific Frequency Matrix and Distance-Bigram Transformation

(2017) et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues

(2017) Jing Yan et al.   NUCLEIC ACIDS RESEARCH

Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism

(2017) Shandar Ahmad et al.   NUCLEIC ACIDS RESEARCH

HMMBinder: DNA-Binding Protein Prediction Using HMM Profile Based Features

(2017) Rianon Zaman et al.   Biomed Research International

“Hit-and-run”: Transcription factors get caught in the act

(2015) Varodom Charoensawan et al.   BIOESSAYS

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

(2015) Ruifeng Xu et al.   BMC Systems Biology

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Transcription factors that interact with p53 and Mdm2

(2015) Kazushi Inoue et al.   INTERNATIONAL JOURNAL OF CANCER

High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder

(2015) Zhenling Peng et al.   NUCLEIC ACIDS RESEARCH

By the company they keep: interaction networks define the binding ability of transcription factors

(2015) Davide Cirillo et al.   NUCLEIC ACIDS RESEARCH

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

(2015) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation

(2015) Bin Liu et al.   Scientific Reports

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

(2015) Zhichao Miao et al.   PLoS Computational Biology

An in silico platform for predicting, screening and designing of antihypertensive peptides

(2015) Ravi Kumar et al.   Scientific Reports

Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes

(2014) K. K. Andrilenas et al.   Briefings in Functional Genomics

Structure-based modeling of protein: DNA specificity

(2014) A. P. Joyce et al.   Briefings in Functional Genomics

Identification of Aim2 as a Sensor for DNA Vaccines

(2014) John J. Suschak et al.   JOURNAL OF IMMUNOLOGY

PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou’s PseAAC and Physicochemical Distance Transformation

(2014) Bin Liu et al.   Molecular Informatics

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes

(2014) Mario Pujato et al.   NUCLEIC ACIDS RESEARCH

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

(2014) Sebastian Horwege et al.   NUCLEIC ACIDS RESEARCH

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

(2014) Wangchao Lou et al.   PLoS One

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

(2014) Bin Liu et al.   PLoS One

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

(2014) Rachael P Huntley et al.   GigaScience

Dipeptide analysis of p53 mutations and evolution of p53 family proteins

(2013) Qiang Huang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Predicting DNA binding proteins using support vector machine with hybrid fractal features

(2013) Xiao-Hui Niu et al.   JOURNAL OF THEORETICAL BIOLOGY

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

(2013) R. Nagarajan et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.)

(2013) Swati Puranik et al.   PLoS One

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

(2013) Rong Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A guide to best practices for Gene Ontology (GO) manual annotation

(2013) R. Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

(2013) Alexandra M. Schnoes et al.   PLoS Computational 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

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Predicting sub-cellular localization of tRNA synthetases from their primary structures

(2011) Bharat Panwar et al.   AMINO ACIDS

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

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

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

SVM based prediction of RNA-binding proteins using binding residues and evolutionary information

(2010) Manish Kumar et al.   JOURNAL OF MOLECULAR RECOGNITION

Convolutional Networks Can Learn to Generate Affinity Graphs for Image Segmentation

(2009) Srinivas C. Turaga et al.   NEURAL COMPUTATION

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

Protein function annotation by homology-based inference

(2009) Yaniv Loewenstein et al.   GENOME BIOLOGY

Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons

(2008) Y.-T. Huang et al.   GENOME RESEARCH

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