Protein design based on parallel dimensional reduction.

G. Moltó 1 Maria Suarez 2, 3 Pablo Tortosa 2 J.M. Alonso 1 V. Hernández 1 A. Jaramillo 2, 3
1 Departamento de Sistemas Informaticos y Computation
2 Programme d'Épigénomique
3 BIOC - Laboratoire de Biochimie de l'Ecole polytechnique
Abstract : The design of proteins with targeted properties is a computationally intensive task with large memory requirements. We have developed a novel approach that combines a dimensional reduction of the problem with a High Performance Computing platform to efficiently design large proteins. This tool overcomes the memory limits of the process, allowing the design of proteins whose requirements prevent them to be designed in traditional sequential platforms. We have applied our algorithm to the design of functional proteins, optimizing for both catalysis and stability. We have also studied the redesign of dimerization interfaces, taking simultaneously into account the stability of the subunits of the dimer. However, our methodology can be applied to any computational chemistry application requiring combinatorial optimization techniques.
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Submitted on : Monday, December 17, 2012 - 3:31:49 PM
Last modification on : Wednesday, March 27, 2019 - 3:56:02 PM

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G. Moltó, Maria Suarez, Pablo Tortosa, J.M. Alonso, V. Hernández, et al.. Protein design based on parallel dimensional reduction.. Journal of Chemical Information and Modeling, American Chemical Society, 2009, 49 (5), pp.1261-71. ⟨10.1021/ci8004594⟩. ⟨hal-00766035⟩

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