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Protein-DNA interaction prediction software tools | Biomolecular structures

Protein-DNA complexes play vital roles in many cellular processes by the interactions of amino acids with DNA. Several computational methods have been developed for predicting the interacting residues in DNA-binding proteins using sequence and/or…
NPIDB
Dataset

NPIDB Nucleic Acids—Protein Interaction DataBase

Provides an access to information about all available structures of…

Provides an access to information about all available structures of DNA–protein and RNA–protein complexes. The NPIDB database contains comparative structural information on some SCOP families. It…

UniPROBE
Dataset

UniPROBE Universal PBM Resource for Oligonucleotide Binding Evaluation

Serves as a convenient source of information on published data generated using…

Serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding…

ProNIT
Dataset

ProNIT

Provides experimentally determined thermodynamic interaction data between…

Provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. ProNIT is useful for researchers wishing to study the underlying mechanisms of protein stability…

BindUP
Web

BindUP

Predicts DNA and RNA binding proteins using a non-homology-based approach.…

Predicts DNA and RNA binding proteins using a non-homology-based approach. BindUP is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP…

NUCPLOT
Desktop

NUCPLOT

Automatically generates schematic diagrams of protein-nucleic acid interactions…

Automatically generates schematic diagrams of protein-nucleic acid interactions for a given PDB file.

DBD-Hunter
Web

DBD-Hunter DNA-Binding Domain Hunter

A knowledge-based method for predicting DNA-binding proteins function from…

A knowledge-based method for predicting DNA-binding proteins function from protein structure.

DRNApred
Web

DRNApred

Predicts the DNA- and RNA-binding proteins. DRNApred is a webserver that…

Predicts the DNA- and RNA-binding proteins. DRNApred is a webserver that accurately and in high-throughput predicts protein–RNA and protein–DNA binding residues from protein sequences. DRNApred…

3D-footprint
Dataset

3D-footprint

A database of DNA-binding protein structures that is updated weekly with…

A database of DNA-binding protein structures that is updated weekly with Protein Data Bank complexes.

DPInteract
Dataset

DPInteract

Catalogues demonstrated sites and non-sites for Escherichia coli DNA-binding…

Catalogues demonstrated sites and non-sites for Escherichia coli DNA-binding proteins. DPInteract is a collection of search matrices from alignments of available experimental proteins. This dataset…

DBSI
Web
Desktop

DBSI DNA Binding Site Identifier

A powerful structure-based SVM model for the prediction and visualization of…

A powerful structure-based SVM model for the prediction and visualization of DNA binding sites on protein structures. DBSI is a machine learning approach to classify surface residues as binders or…

DP-Bind
Web

DP-Bind

A web server for predicting DNA-binding sites in a DNA-binding protein from its…

A web server for predicting DNA-binding sites in a DNA-binding protein from its amino acid sequence. The web server implements three machine learning methods: support vector machine, kernel logistic…

DNABINDPROT
Web

DNABINDPROT

Designed to predict DNA-binding residues, based on the fluctuations of residues…

Designed to predict DNA-binding residues, based on the fluctuations of residues in high-frequency modes by the Gaussian network model.

fABMACS
Desktop

fABMACS fast Adaptively Biased MAchine for Chemical Simulations

An implementation of adaptive biasing that greatly improves the speed of free…

An implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. fABMACS will be useful in identification of false positives,…

hPDI
Web

hPDI Human Protein-DNA Interactome

Holds experimental protein-DNA interaction data for humans identified by…

Holds experimental protein-DNA interaction data for humans identified by protein microarray assays.

DR_bind
Web

DR_bind

Permits users to predict DNA-binding residues. DR_bind makes predictions by…

Permits users to predict DNA-binding residues. DR_bind makes predictions by spotting solvent-accessible residues, a cluster of conserved and electrostatically stabilized. It offers users the…

BIPA
Dataset

BIPA Biological Interaction database for Protein-nucleic Acid

Stores protein-nucleic acid interaction. BIPA is a database that provides…

Stores protein-nucleic acid interaction. BIPA is a database that provides various features of protein–nucleic acid interfaces and non-redundant multiple structural alignments for nucleic…

PNImodeler
Web

PNImodeler Protein-Nucleic acid Interaction modeler

Predicts protein binding nucleotides in DNA. PNImodeler is a web server which…

Predicts protein binding nucleotides in DNA. PNImodeler is a web server which consists of two models: one model uses DNA sequence data alone and predicts all potential binding sites with unknown…

DBD-Threader
Web

DBD-Threader

A program for predicting the DNA-binding function of a protein. The program is…

A program for predicting the DNA-binding function of a protein. The program is a threading-based approach that requires only sequence as input. If the protein is predicted as DNA-binding, the program…

PSFM-DBT
Web

PSFM-DBT Position Specific Frequency Matrix-Distance-Bigram Transformation

Recognizes DNA binding proteins (iDBPs) by using Distance-Bigram Transformation…

Recognizes DNA binding proteins (iDBPs) by using Distance-Bigram Transformation (DBT) method. PSFM-DBT calculates the occurrence frequency of a combination of two amino acids separated by a certain…

iDBPs
Web

iDBPs

Uses the three-dimensional (3D) structure of a query protein to predict whether…

Uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA.

BindN+
Web

BindN+

An upgraded version of BindN, applies support vector machines (SVMs) to…

An upgraded version of BindN, applies support vector machines (SVMs) to sequence-based prediction of DNA or RNA-binding residues from biochemical features and evolutionary information.

PDBparam
Web

PDBparam

Computes more than 50 structure-based features for any given protein structure.…

Computes more than 50 structure-based features for any given protein structure. PDBparam can deal with inter residue interactions, amino acid propensities, physicochemical properties, and binding…

DP-dock
Web

DP-dock

This is a web server implementation of a method for predicting DNA-binding…

This is a web server implementation of a method for predicting DNA-binding proteins residues and DNA-protein binding modes.

EL_PSSM-RT
Web
TFmodeller
Web

TFmodeller

Exploits the current knowledge about protein-DNA interfaces contained in the…

Exploits the current knowledge about protein-DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology.

SABINE
Web
Desktop

SABINE Stand-Alone BINding specificity Estimator

Predicts the binding specificity of a transcription factor (TF), given its…

Predicts the binding specificity of a transcription factor (TF), given its amino acid sequence, DNA-binding domains, superclass and species. SABINE compares a given transcription factor to a…

TFpredict
Web
Desktop

TFpredict

Identifies transcription factors (TFs), predicts their structural superclass,…

Identifies transcription factors (TFs), predicts their structural superclass, and detects their DNA-binding domains given a protein sequence of interest. TFpredict is implemented in a Java…

ContPro
Web

ContPro

Calculates amino acid contact distances in proteins at different distance…

Calculates amino acid contact distances in proteins at different distance threshold from the 3 Dimensional (3D)-structure of the protein. ContPro calculates the distance between selected protein…

WebPDA
Web
DBD2BS
Web

DBD2BS

Uses the structure of DNA binding domains (DBDs) to predict the corresponding…

Uses the structure of DNA binding domains (DBDs) to predict the corresponding binding sites on DNA.

SAMPDI
Web
ThreaDNA
Desktop

ThreaDNA

Provides genome-wide deformation energy profiles. ThreaDNA is a package that…

Provides genome-wide deformation energy profiles. ThreaDNA is a package that implements a systematic approach to estimate the latter contribution for a large class of nucleoprotein complexes. This…

HDOCK
Web

HDOCK

Provides a user-friendly web access to a hybrid algorithm of template-based…

Provides a user-friendly web access to a hybrid algorithm of template-based modeling and free docking for protein-protein and protein-DNA/RNA complexes. HDOCK is a docking server that efficiently…

INTAA
Web

INTAA

Calculates protein residue Interaction Energy Matrix of amino acids between…

Calculates protein residue Interaction Energy Matrix of amino acids between themselves and with deoxyribonucleotides. INTAA permits to make analysis of the interfaces in protein–DNA complexes. It…

Local-DPP
Web

Local-DPP

Addresses the challenging problem of discretizing protein sequences such that…

Addresses the challenging problem of discretizing protein sequences such that DNA-binding proteins and non-DNA-binding proteins. Local-DPP is a machine learning-based method which predicts…

DNAproDB
Dataset

DNAproDB

Performs structure analysis of DNA–protein complexes and extract structural…

Performs structure analysis of DNA–protein complexes and extract structural features from the complex via an automated structure-processing pipeline. DNAproDB provides a database of DNA–protein…

LigParGen
Web

LigParGen

Provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force…

Provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field (FF) parameters for organic ligands. LigParGen is a web server which generates ligand parameters for common…

Multi-VORFFIP
Web

Multi-VORFFIP

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding…

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding sites. Multi-VORFFIP utilizes a wide range of structural, evolutionary, experimental and energy-based information that…

PDIviz
Desktop

PDIviz

A plugin for the PyMOL molecular visualization system that analyzes protein-DNA…

A plugin for the PyMOL molecular visualization system that analyzes protein-DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free…

CONSRANK
Web

CONSRANK CONSensus-RANKing

A web tool for analyzing, comparing and ranking protein-protein and…

A web tool for analyzing, comparing and ranking protein-protein and protein-nucleic acid docking models, based on the conservation of inter-residue contacts and its visualization in 2D and 3D…

gDNA-Prot
Desktop

gDNA-Prot

Predicts DNA-binding proteins. gDNA-Prot is a DNA-binding predictor that…

Predicts DNA-binding proteins. gDNA-Prot is a DNA-binding predictor that combines the support vector machine classifier and a novel kind of feature called graphical representation. The method is…

JET
Desktop

JET Joint Evolutionary Trees

Detects very different types of interactions of a protein with another protein,…

Detects very different types of interactions of a protein with another protein, ligands, DNA, and RNA. JET, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary…

SPOT-Struct-DNA
Web

SPOT-Struct-DNA

A highly reliable computational technique for predicting DNA-binding function…

A highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most…

PFplus
Web

PFplus Patch Finder Plus

A web-based tool for extracting and displaying continuous electrostatic…

A web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate…

DISPLAR
Web

DISPLAR

A neural network method. Given the structure of a protein known to bind DNA,…

A neural network method. Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA. The inputs to the neural network include position-specific sequence…

BindN
Web

BindN

Applies support vector machines (SVMs) to prediction of DNA and RNA-binding…

Applies support vector machines (SVMs) to prediction of DNA and RNA-binding residues from sequence features, including the side chain pKa value, hydrophobicity index and molecular mass of an amino…

ProteDNA
Web

ProteDNA

A sequence-based predictor for identifying the sequence-specific binding…

A sequence-based predictor for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein-DNA interactions, there are two types of binding mechanisms…

CNNsite
Desktop

CNNsite

Classifies neural network. CNNsite combines the motif features captured by…

Classifies neural network. CNNsite combines the motif features captured by Convolutional Neural Network (CNN), the sequence features and the evolutionary features. It uses a window based approach.…

DeeperBind
Desktop

DeeperBind

Predicts protein-DNA binding affinity from high-throughput assays that measure…

Predicts protein-DNA binding affinity from high-throughput assays that measure the binding affinity. DeeperBind is a long short term recurrent convolutional network for prediction of protein binding…

PDNAsite
Web

PDNAsite

A web application for the identification of DNA-binding site from protein…

A web application for the identification of DNA-binding site from protein sequence by incorporating spatial and sequence context. PDNAsite was developed through the integration of the support vector…

PDSA
Dataset

PDSA Protein-DNA Structure-Affinity Database

Contains protein-DNA structural complexes. PDSA is suitable for general use in…

Contains protein-DNA structural complexes. PDSA is suitable for general use in the analysis of the relationship between sequence and structure. It can assist users to retrieve helix-turn-helix…

PSSM-DT
Web

PSSM-DT PSSM Distance Transformation

A web server for identifying DNA-binding proteins from sequence by combining…

A web server for identifying DNA-binding proteins from sequence by combining SVM and PSSM-DT. The PSSM-DT is the features from PSSM by considering the probabilities of pairs of amino acid separated…

TargetSOS
Web

TargetSOS Target Supervised Over-Sampling

Predicts protein-nucleotide binding residue. TargetSOS synthesizes additional…

Predicts protein-nucleotide binding residue. TargetSOS synthesizes additional minority class samples to address class imbalance. The experimental results from protein-nucleotide interaction datasets…

iDNA-Prot|dis
Web

iDNA-Prot|dis

With the avalanche of protein sequences generated in the postgenomic age, it is…

With the avalanche of protein sequences generated in the postgenomic age, it is a critical challenge to develop automated methods for accurate and rapidly identifying DNA-binding proteins based on…

iDNA-Prot
Web

iDNA-Prot

Predicts DNA-binding proteins. iDNA-Prot is a classifier which can be used to…

Predicts DNA-binding proteins. iDNA-Prot is a classifier which can be used to predict whether a protein can bind with DNA according to its sequence information alone. The jack-knife cross-validation…

PseDNA-Pro
Web

PseDNA-Pro

A feature vector - composed of three kinds of sequence-based features,…

A feature vector - composed of three kinds of sequence-based features, including overall amino acid composition, pseudo amino acid composition (PseAAC) proposed by Chou and physicochemical distance…

iDNAPro-PseAAC
Web

iDNAPro-PseAAC

A predictor for identifying DNA-binding proteins only based on the sequence…

A predictor for identifying DNA-binding proteins only based on the sequence information of proteins. iDNAPro-PseAAC extends the classic PseAAC approach by incorporating the evolutionary information…

NuProPlot
Desktop

NuProPlot

Automatically identify hydrogen, electrostatic and van der Waals interactions…

Automatically identify hydrogen, electrostatic and van der Waals interactions between proteins and nucleic acids and generate a plot showing all of the interactions. Protein-DNA and protein-RNA…

TeloPIN
Dataset

TeloPIN Telomeric Proteins Interaction Network

A database that points to provide comprehensive information on protein-protein,…

A database that points to provide comprehensive information on protein-protein, protein-DNA and protein-RNA interaction of telomeres. TeloPIN database contains four types of interaction data,…

DBindR
Web

DBindR

A computational approach for predicting DNA-binding sites in proteins from…

A computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank…

DBS-PRED
Web

DBS-PRED

Predicts the DNA-binding in a protein from their sequence information. Two…

Predicts the DNA-binding in a protein from their sequence information. Two neighbours of each residue are taken as the input information and using information from known binding sites of proteins,…

COCOMAPS
Web

COCOMAPS bioCOmplexes COntact MAPS

A web application to easily and effectively analyse and visualize the interface…

A web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of…

nDNA-Prot
Web

nDNA-Prot

An ensemble classification algorithm to improve the identification of…

An ensemble classification algorithm to improve the identification of DNA-binding proteins. nDNA-Prot framework is comprised of two stages: a 188-dimension feature extraction method to obtain the…

enDNA-Prot
Web

enDNA-Prot

A web server for identifying DNA-binding proteins by applying ensemble…

A web server for identifying DNA-binding proteins by applying ensemble learning. enDNA-Prot firstly encoded each protein sequence into a feature vector with dimension of 188 with features only…

newDNA-Prot
Desktop

newDNA-Prot

A DNA-binding protein predictor that employs support vector machine classifier…

A DNA-binding protein predictor that employs support vector machine classifier and a comprehensive feature representation. The sequence representation are categorized into 6 groups: primary sequence…

BindN-RF
Web

BindN-RF

Applies random forests (RFs) to sequence-based prediction of DNA-binding…

Applies random forests (RFs) to sequence-based prediction of DNA-binding residues in proteins using biochemical features and evolutionary information. The RF classifier has been constructed using the…

DNABind
Web

DNABind

Accurate prediction of DNA-binding residues has become a problem of increasing…

Accurate prediction of DNA-binding residues has become a problem of increasing importance in structural bioinformatics. DNABind is a hybrid algorithm for identifying these crucial residues by…

DNAbinder
Web

DNAbinder

A web server for predicting DNA-binding proteins from their amino acid…

A web server for predicting DNA-binding proteins from their amino acid sequence. First, we analyzed the amino acid composition of DNA-binding proteins and based on the observation, SVM models have…

DBS-PSSM
Web

DBS-PSSM

A neural network based algorithm to utilize evolutionary information of amino…

A neural network based algorithm to utilize evolutionary information of amino acid sequences in terms of their position specific scoring matrices (PSSMs) for a better prediction of DNA-binding sites.…

CONS-COCOMAPS
Web

CONS-COCOMAPS CONSensun COCOMAPS

A tool to easily measure and visualize the consensus in multiple docking…

A tool to easily measure and visualize the consensus in multiple docking solutions. It uses the conservation of inter-residue contacts as an estimate of the similarity between different docking…

MetaDBSite
Web

MetaDBSite

A meta web server to predict DNA-binding residues for DNA-binding proteins.…

A meta web server to predict DNA-binding residues for DNA-binding proteins. MetaDBSite integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, BindN-rf,…

DBBP
Dataset
Sliding Box…
Desktop

Sliding Box Docking

Manages simulations of ligand docking at different defined positions of a…

Manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. Sliding Box Docking manages docking simulations of one ligand into a box that slides along…

DNABR
Web

DNABR DNA Binding Residues

A method for predicting DNA-binding residues in protein sequences using the…

A method for predicting DNA-binding residues in protein sequences using the random forest (RF) classifier with sequence-based features. Performance comparisons with other approaches clearly show that…

JonesEtAl2003
Web

JonesEtAl2003

Allows users to predict DNA binding function from structure using 3-dimensional…

Allows users to predict DNA binding function from structure using 3-dimensional (3D) templates. This method uses 3D structural templates to identify proteins that have a specific DNA binding…

3DTF
Web

3DTF 3D Transcription Factor

A web-server to analyze the protein-DNA binding site and calculate Positional…

A web-server to analyze the protein-DNA binding site and calculate Positional weight matrix (PWM), representing the DNA-binding specifity of the protein.

PreDNA
Web

PreDNA

Predicts DNA-binding sites in proteins. PreDNA is a webserver implementing a…

Predicts DNA-binding sites in proteins. PreDNA is a webserver implementing a computational method based on support vector machine (SVM) and geometric structure-based algorithms. The final results are…

Nucleos
Web

Nucleos

A web server for the identification of nucleotide-binding sites in protein…

A web server for the identification of nucleotide-binding sites in protein structures. Nucleos compares the structure of a query protein against a set of known template 3D binding sites representing…

NAPS
Web

NAPS

A method for the identification of amino acid residues involved in DNA- and…

A method for the identification of amino acid residues involved in DNA- and RNA-binding using sequence-based attributes. NAPS used in this work combines the C4.5 algorithm with bootstrap aggregation…

SNBRFinder
Web

SNBRFinder Sequence-based Nucleic acid-Binding Residue Finder

A sequence-based hybrid algorithm for predicting nucleic acid-binding residues.…

A sequence-based hybrid algorithm for predicting nucleic acid-binding residues. To address this problem, the profile HMM alignment was ingeniously utilized to establish the sequence-based template…

DISIS
Desktop

DISIS

A tool for predicting binding sites even in the absence of any experimental…

A tool for predicting binding sites even in the absence of any experimental information (in particular, without using 3D structures), in the absence of annotations and even in the absence of…

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