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A Novel Multi-objectivisation Approach for Optimising the Protein Inverse Folding Problem
Nielsen, Sune Steinbjorn; Danoy, Grégoire; Jurkowski, Wiktor et al.
2015In Applications of Evolutionary Computation: 18th European Conference, EvoApplications 2015, Copenhagen, Denmark, April 8-10, 2015, Proceedings
Peer reviewed
 

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Keywords :
Inverse Folding Problem; Genetic Algorithm; Multi-objectivisation
Abstract :
[en] In biology, the subject of protein structure prediction is of continued interest, not only to chart the molecular map of the living cell, but also to design proteins of new functions. The Inverse Folding Problem (IFP) is in itself an important research problem, but also at the heart of most rational protein design approaches. In brief, the IFP consists in finding sequences that will fold into a given structure, rather than determining the structure for a given sequence - as in conventional structure prediction. In this work we present a Multi Objective Genetic Algorithm (MOGA) using the diversity-as-objective (DAO) variant of multi-objectivisation, to optimise secondary structure similarity and sequence diversity at the same time, hence pushing the search farther into wide-spread areas of the sequence solution-space. To control the high diversity generated by the DAO approach, we add a novel Quantile Constraint (QC) mechanism to discard an adjustable worst quantile of the population. This DAO-QC approach can efficiently emphasise exploitation rather than exploration to a selectable degree achieving a trade-off producing both better and more diverse sequences than the standard Genetic Algorithm (GA). To validate the final results, a subset of the best sequences was selected for tertiary structure prediction. The super-positioning with the original protein structure demonstrated that meaningful sequences are generated underlining the potential of this work.
Research center :
ULHPC - University of Luxembourg: High Performance Computing
Disciplines :
Computer science
Author, co-author :
Nielsen, Sune Steinbjorn ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC)
Danoy, Grégoire  ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC)
Jurkowski, Wiktor;  TGAC, Norwich Research Park, Norwich, UK
Jimenez Laredo, Juan Luis;  LITIS, Universite du Havre, Le Havre, France
Schneider, Reinhard ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Talbi, El-Ghazali
Bouvry, Pascal ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC)
External co-authors :
yes
Language :
English
Title :
A Novel Multi-objectivisation Approach for Optimising the Protein Inverse Folding Problem
Publication date :
2015
Event name :
18th European Conference on the Applications of Evolutionary Computation
Event place :
Copenhagen, Denmark
Event date :
from 08-04-2015 to 10-04-2015
Audience :
International
Main work title :
Applications of Evolutionary Computation: 18th European Conference, EvoApplications 2015, Copenhagen, Denmark, April 8-10, 2015, Proceedings
Peer reviewed :
Peer reviewed
Focus Area :
Computational Sciences
Funders :
FNR - Fonds National de la Recherche [LU]
Available on ORBilu :
since 29 February 2016

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