Document Detail


Protein design based on parallel dimensional reduction.
MedLine Citation:
PMID:  19422245     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Germán Moltó; María Suárez; Pablo Tortosa; José M Alonso; Vicente Hernández; Alfonso Jaramillo
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of chemical information and modeling     Volume:  49     ISSN:  1549-9596     ISO Abbreviation:  -     Publication Date:  2009 May 
Date Detail:
Created Date:  2009-06-29     Completed Date:  2009-07-14     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101230060     Medline TA:  J Chem Inf Model     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1261-71     Citation Subset:  IM    
Affiliation:
Departamento de Sistemas Informáticos y Computación, Universidad Politécnica de Valencia, 46022 Valencia, Spain.
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MeSH Terms
Descriptor/Qualifier:
Dimerization
Protein Folding
Proteins / chemistry*
Chemical
Reg. No./Substance:
0/Proteins

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