Protein design based on parallel dimensional reduction

Germán Moltó, María Suárez, Pablo Tortosa, José M Alonso, Vicente Hernández, and Alfonso Jaramillo. Protein design based on parallel dimensional reduction. Journal of chemical information and modeling, 49:1261–71, 5 2009.

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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.

BibTeX Entry

@article{Molto2009pdb,
   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.},
   author = {Germán Moltó and María Suárez and Pablo Tortosa and José M Alonso and Vicente Hernández and Alfonso Jaramillo},
   doi = {10.1021/ci8004594},
   issn = {1549-9596},
   issue = {5},
   journal = {Journal of chemical information and modeling},
   keywords = {Dimerization,Protein Folding,Proteins,Proteins: chemistry},
   month = {5},
   pages = {1261-71},
   pmid = {19422245},
   title = {Protein design based on parallel dimensional reduction},
   volume = {49},
   year = {2009}
}