Links
Useful links to resources related to protein-DNA interaction are available below.
3d-footprint
Collection of PWM extracted from structure.
3DNA
Tool for extracting DNA structure parameters.
AANT
Collection of amino acid-nucleotide interactions derived from experimentally determined protein?nucleic acid structures.
BindN
SVM-based tool for prediction of DNA and RNA binding residues in protein.
BIPA
Database for protein?nucleic acid interactions in 3D structures. It provides various features of protein-nucleic acid interfaces.
Curves+
Tool for extracting DNA structure parameters.
DNABindR
Web server for identification of DNA binding residues in protein sequences.
DP-Bind
Web-server that takes a sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA.
hPDI
Database that holds experimental protein?DNA interaction data for humans identified by protein microarray assays.
IAlign
Software to align protein-DNA interfaces based on a matrix score.
JASPAR
Open-access database for eukaryotic transcription factor binding profiles.
NDB
The nucleic acid database.
NPIDB
Database containing information derived from structures of DNA-protein and RNA-protein complexes extracted from PDB.
NUCPLOT
Programme to generate schematic diagrams of protein-nucleic acid interactions.
PDA
Automatic programme for the analysis of protein-DNA complex structures.
PDBSum
Web-based database of summaries and analyses of all PDB structures.
ProNIT
Database that collects experimentally observed binding data from the literature. It contains several important thermodynamic data for protein-nucleic acid binding.
ProNuC
Database containing structural data of protein-nucleic acid complex. The data are classified according to recognition motif of proteins and DNA forms involved in the complex.
ProtNA-ASA
Database that combines the data on conformational parameters of nucleic acids and accessible surface area of nucleic acid atoms in protein-DNA/RNA complexes.
Tfmodeller
Programme for comparative modelling of protein-DNA complexes.
TRANSFAC
Private database for eukaryotic transcription factor binding profiles.
ZifBase
Collection of various natural and engineered zinc finger proteins, containing sequence features and linked to their structures.
3d-footprint
Collection of PWM extracted from structure.
3DNA
Tool for extracting DNA structure parameters.
AANT
Collection of amino acid-nucleotide interactions derived from experimentally determined protein?nucleic acid structures.
BindN
SVM-based tool for prediction of DNA and RNA binding residues in protein.
BIPA
Database for protein?nucleic acid interactions in 3D structures. It provides various features of protein-nucleic acid interfaces.
Curves+
Tool for extracting DNA structure parameters.
DNABindR
Web server for identification of DNA binding residues in protein sequences.
DP-Bind
Web-server that takes a sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA.
hPDI
Database that holds experimental protein?DNA interaction data for humans identified by protein microarray assays.
IAlign
Software to align protein-DNA interfaces based on a matrix score.
JASPAR
Open-access database for eukaryotic transcription factor binding profiles.
NDB
The nucleic acid database.
NPIDB
Database containing information derived from structures of DNA-protein and RNA-protein complexes extracted from PDB.
NUCPLOT
Programme to generate schematic diagrams of protein-nucleic acid interactions.
PDA
Automatic programme for the analysis of protein-DNA complex structures.
PDBSum
Web-based database of summaries and analyses of all PDB structures.
ProNIT
Database that collects experimentally observed binding data from the literature. It contains several important thermodynamic data for protein-nucleic acid binding.
ProNuC
Database containing structural data of protein-nucleic acid complex. The data are classified according to recognition motif of proteins and DNA forms involved in the complex.
ProtNA-ASA
Database that combines the data on conformational parameters of nucleic acids and accessible surface area of nucleic acid atoms in protein-DNA/RNA complexes.
Tfmodeller
Programme for comparative modelling of protein-DNA complexes.
TRANSFAC
Private database for eukaryotic transcription factor binding profiles.
ZifBase
Collection of various natural and engineered zinc finger proteins, containing sequence features and linked to their structures.