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

id	todo:paper_00766879_v498_n_p3_Nadra
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spelling	todo:paper_00766879_v498_n_p3_Nadra2023-10-03T14:54:12Z DNA-binding specificity prediction with FoldX Nadra, A.D. Serrano, L. Alibés, A. 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 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. Fil:Nadra, A.D. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. SER info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_00766879_v498_n_p3_Nadra
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	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
spellingShingle	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 Nadra, A.D. Serrano, L. Alibés, A. DNA-binding specificity prediction with FoldX
topic_facet	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
description	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.
format	SER
author	Nadra, A.D. Serrano, L. Alibés, A.
author_facet	Nadra, A.D. Serrano, L. Alibés, A.
author_sort	Nadra, A.D.
title	DNA-binding specificity prediction with FoldX
title_short	DNA-binding specificity prediction with FoldX
title_full	DNA-binding specificity prediction with FoldX
title_fullStr	DNA-binding specificity prediction with FoldX
title_full_unstemmed	DNA-binding specificity prediction with FoldX
title_sort	dna-binding specificity prediction with foldx
url	http://hdl.handle.net/20.500.12110/paper_00766879_v498_n_p3_Nadra
work_keys_str_mv	AT nadraad dnabindingspecificitypredictionwithfoldx AT serranol dnabindingspecificitypredictionwithfoldx AT alibesa dnabindingspecificitypredictionwithfoldx
_version_	1807317972016955392

DNA-binding specificity prediction with FoldX

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