A Novel Multi-objectivisation Approach for Optimising the Protein Inverse Folding Problem

Nielsen, Sune S.; Danoy, Grégoire; Jurkowski, Wiktor; Laredo, Juan Luís Jiménez; Schneider, Reinhard; Talbi, El‐Ghazali; Bouvry, Pascal

doi:10.1007/978-3-319-16549-3_2

Cited by 5 publications

(5 citation statements)

References 21 publications

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“…A number of studies (Brown et al, 2015;Nielsen et al, 2015) discussed various approximate methods for protein folding calculations. In particular, statistical methods, the bat algorithm, swarm intelligence, genetic algorithms and others were considered.…”

Section: Introductionmentioning

confidence: 99%

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

Melkikh

Meijer

2018

Progress in Biophysics and Molecular Biology

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The current protein folding literature is reviewed. Two main approaches to the problem of folding were selected for this review: geometrical and biophysical. The geometrical approach allows the formulation of topological restrictions on folding, that are usually not taken into account in the construction of physical models. In particular, the topological constraints do not allow the known funnel-like energy landscape modeling, although most common methods of resolving the paradox are based on this method. The very paradox is based on the fact that complex molecules must reach their native conformations (complexes that result from reactions) in an exponentially long time, which clearly contradicts the observed experimental data. In this respect we considered the complexity of the reactions between ligands and proteins. On this general basis, the folding-reaction paradox was reformulated and generalized. We conclude that prospects for solving the paradox should be associated with incorporating a topology aspect in biophysical models of protein folding, through the construction of hybrid models. However, such models should explicitly include long-range force fields and local cell biological conditions, such as structured water complexes and photon/phonon/soliton waves, ordered in discrete frequency bands. In this framework, collective and coherent oscillations in, and between, macromolecules are instrumental in inducing intra- and intercellular resonance, serving as an integral guiding network of life communication: the electrome aspect of the cell. Yet, to identify the actual mechanisms underlying the bonds between molecules (atoms), it will be necessary to perform dedicated experiments to more definitely solve the particular time paradox.

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Section: Introductionmentioning

confidence: 99%

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

Melkikh

Meijer

2018

Progress in Biophysics and Molecular Biology

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“…In the current work it was chosen such that C R pred + max R pred = 20. By using the objective function Fsec(A) in Equation 2 as target for optimisation algorithms, likely solutions to the IFP have been found [4]. The next section essentially presents an alternative lightweight function designed to have very similar properties.…”

Section: Protein Inverse Folding Problemmentioning

confidence: 99%

“…Analysis of epistatic links among model variables is another important way of characterising a problem instance, which will be described in the following. As protein sample for the IFP, only 1b3a is considered as previous work [4] has suggested that different protein samples show very similar characteristics.…”

Section: Landscape Analysismentioning

confidence: 99%

“…As a final comparison, the two NKL Models and the IFP are solved with a standard Genetic Algorithm (GA) and the NSGAII with Diversity-as-Objective and Quantile Constraint (NSGAII-DAO-QC) algorithm proposed in [4]. The main feature of the latter algorithm is to maintain a high and controllable degree of diversity which allows studying the exploration-exploitation trade-off.…”

Section: Evolutionary Algorithm Analysismentioning

confidence: 99%

“…In practice researchers focus on finding a limited number of new matching sequences which are as different as possible from the original reference sequence. The inverse folding problem has been tackled in [4] where a simplified model was developed to matching solely the reference secondary structure -a requirement for the tertiary structure to match. This is motivated by the fact that computing the tertiary, i.e.…”

Section: Protein Inverse Folding Problemmentioning

confidence: 99%

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NK Landscape Instances Mimicking the Protein Inverse Folding Problem Towards Future Benchmarks

Nielsen

Danoy

Bouvry

et al. 2015

Proceedings of the Companion Publication of the 2015 Annual Conference on Genetic and Evolutionary Computation

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This paper introduces two new nominal NK Landscape model instances designed to mimic the properties of one challenging optimisation problem from biology: the Inverse Folding Problem (IFP), here focusing on a simpler secondary structure version. Through landscape analysis tests, numerous problem properties are identified and used to parameterise and validate model instances in terms of epistatic links, adaptive-and random walk characteristics. Then the performance of different Genetic Algorithms (GAs) is compared on both the new NK Models and the original IFP, in terms of population diversity, solution quality and convergence characteristics. It is demonstrated that very similar properties are captured in all presented tests with a significantly faster evaluation time compared to the real IFP. The future purpose of such a model is to provide a generic benchmark for algorithms targeting protein sequence optimisation, specifically in protein design. It may also provide the foundation for more in-depth studies of the size, shape and characteristics of the solution space of good solutions to the IFP.

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Using multi-objective evolutionary algorithms for single-objective constrained and unconstrained optimization

et al. 2015

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A Novel Multi-objectivisation Approach for Optimising the Protein Inverse Folding Problem

Cited by 5 publications

References 21 publications

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

NK Landscape Instances Mimicking the Protein Inverse Folding Problem Towards Future Benchmarks

Using multi-objective evolutionary algorithms for single-objective constrained and unconstrained optimization

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