DNA-binding specificity prediction with FoldX

With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wi...

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Detalles Bibliográficos
Autores principales: Nadra, A.D., Serrano, L., Alibés, A.
Formato: SER
Materias:
adenine
algorithm
article
base pairing
computer prediction
DNA binding
DNA determination
DNA strand
DNA structure
nuclear magnetic resonance
nucleotide sequence
priority journal
protein DNA interaction
Algorithms
Base Sequence
Binding Sites
DNA
Molecular Sequence Data
Molecular Structure
Mutation
Protein Binding
Protein Conformation
Protein Folding
Proteins
Sensitivity and Specificity
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_00766879_v498_n_p3_Nadra
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
Descripción
Sumario:With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wild-type protein or design new specificities by using the protein design algorithm FoldX. The only basic requirement is having a good resolution structure of the complex. Protein-DNA interaction design may aid the development of new parts designed to be orthogonal, decoupled, and precise in its target. Further, it could help to fine-tune the systems in terms of specificity, discrimination, and binding constants. In the age of newly developed devices and invented systems, computer-aided engineering promises to be an invaluable tool. © 2011 Elsevier Inc. All rights reserved.

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