:: DESCRIPTION
PreDBA is a computational method that can effectively predict Protein-DNA Binding Affinity using Machine Learning Algorithm.
::DEVELOPER
DLab (Data Mining and Bioinformatics Lab)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yang W, Deng L.
PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity.
Sci Rep. 2020 Jan 28;10(1):1278. doi: 10.1038/s41598-020-57778-1. PMID: 31992738; PMCID: PMC6987227.
:: DESCRIPTION
intf_model (The program interface model) can be used predict the conformation of the sidechains within a protein-DNA binding interface as described in Siggers and Honig, (2007) Nucl. Acid Res. 35:1085-1097.. The program allows the identity of the amino acid and base residues in the interface to be changed by the user. Generating multiple, modeled protein-DNA complexes by modeling the binding interface of a protein-DNA complex with multiple DNA sequences, followed by a binding energy calculation on the modeled complexes, provides a way to predict the binding specificity of a protein for different DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Siggers & Honig (2007)
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry
Nucl. Acid Res. 35:1085-1097
