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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.


Documento: Artículo
Título:DNA-binding specificity prediction with FoldX
Autor:Nadra, A.D.; Serrano, L.; Alibés, A.
Filiación:Departamentos de Quimica Biologica y Fisiologia, Biologia Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
EMBL/CRG Systems Biology Research Unit, Center for Genomic Regulation (CRG), UPF, Barcelona, Spain
Palabras clave: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
Página de inicio:3
Página de fin:18
Título revista:Methods in Enzymology
Título revista abreviado:Methods Enzymol.
CAS:adenine, 22177-51-1, 2922-28-3, 73-24-5; DNA, 9007-49-2; Proteins


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---------- APA ----------
Nadra, A.D., Serrano, L. & Alibés, A. (2011) . DNA-binding specificity prediction with FoldX. Methods in Enzymology, 498, 3-18.
---------- CHICAGO ----------
Nadra, A.D., Serrano, L., Alibés, A. "DNA-binding specificity prediction with FoldX" . Methods in Enzymology 498 (2011) : 3-18.
---------- MLA ----------
Nadra, A.D., Serrano, L., Alibés, A. "DNA-binding specificity prediction with FoldX" . Methods in Enzymology, vol. 498, 2011, pp. 3-18.
---------- VANCOUVER ----------
Nadra, A.D., Serrano, L., Alibés, A. DNA-binding specificity prediction with FoldX. Methods Enzymol. 2011;498:3-18.