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Nucleic Acids Res. 2016 Jul 8;44(W1):W568-74. doi: 10.1093/nar/gkw454. Epub 2016 May 19.

BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

Author information

1
Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.
2
Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel yaelmg@tx.technion.ac.il.

Abstract

Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with yet another known function, are awaiting to be discovered. Here we present a new web server, BindUP, freely accessible through the website http://bindup.technion.ac.il/, for predicting DNA and RNA binding proteins using a non-homology-based approach. Our method is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP predicts nucleic acid binding function given the proteins three-dimensional structure or a structural model. Additionally, BindUP provides information on the largest electrostatic surface patches, visualized on the server. The server was tested on several datasets of DNA and RNA binding proteins, including proteins which do not possess DNA or RNA binding domains and have no similarity to known nucleic acid binding proteins, achieving very high accuracy. BindUP is applicable in either single or batch modes and can be applied for testing hundreds of proteins simultaneously in a highly efficient manner.

PMID:
27198220
PMCID:
PMC4987955
DOI:
10.1093/nar/gkw454
[Indexed for MEDLINE]
Free PMC Article

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