A review of evolutionary algorithms for computing functional conformations of protein molecules
A Shehu - Computer-aided drug discovery, 2016 - Springer
The ubiquitous presence of proteins in chemical pathways in the cell and their key role in
many human disorders motivates a growing body of protein modeling studies to unravel the …
many human disorders motivates a growing body of protein modeling studies to unravel the …
[HTML][HTML] Niching methods integrated with a differential evolution memetic algorithm for protein structure prediction
D Varela, J Santos - Swarm and Evolutionary Computation, 2022 - Elsevier
A memetic version between an evolutionary algorithm (differential evolution) and the local
search provided by protein fragment replacements was defined for protein structure …
search provided by protein fragment replacements was defined for protein structure …
Multi-objective stochastic search for sampling local minima in the protein energy surface
B Olson, A Shehu - Proceedings of the International Conference on …, 2013 - dl.acm.org
We present an evolutionary stochastic search algorithm to obtain a discrete representation
of the protein energy surface in terms of an ensemble of conformations representing local …
of the protein energy surface in terms of an ensemble of conformations representing local …
Generating, maintaining, and exploiting diversity in a memetic algorithm for protein structure prediction
Computational approaches to de novo protein tertiary structure prediction, including those
based on the preeminent “fragment-assembly” technique, have failed to scale up fully to …
based on the preeminent “fragment-assembly” technique, have failed to scale up fully to …
Protein structure prediction in an atomic model with differential evolution integrated with the crowding niching method
D Varela, J Santos - Natural Computing, 2022 - Springer
A hybrid version between differential evolution and the fragment replacement technique was
defined for protein structure prediction. The coarse-grained atomic model of the Rosetta …
defined for protein structure prediction. The coarse-grained atomic model of the Rosetta …
A memetic algorithm for 3D protein structure prediction problem
L Correa, B Borguesan, C Farfán… - … ACM transactions on …, 2016 - ieeexplore.ieee.org
Memetic Algorithms are population-based metaheuristics intrinsically concerned with
exploiting all available knowledge about the problem under study. The incorporation of …
exploiting all available knowledge about the problem under study. The incorporation of …
A novel population-based optimization for multiple sequence alignment in protein sequencing
This paper proposes a novel Population-based optimization (PBO) approach to use in
conjunction with an upgraded migration operator. It can tackle multiple sequence alignment …
conjunction with an upgraded migration operator. It can tackle multiple sequence alignment …
A multi-population memetic algorithm for the 3-D protein structure prediction problem
L de Lima Corrêa, M Dorn - Swarm and Evolutionary Computation, 2020 - Elsevier
In this paper, we present a knowledge-based memetic algorithm to tackle the three-
dimensional protein structure prediction problem without the explicit use of experimentally …
dimensional protein structure prediction problem without the explicit use of experimentally …
[HTML][HTML] Three-dimensional protein structure prediction based on memetic algorithms
Tertiary protein structure prediction is a challenging problem in Structural Bioinformatics and
is classified according to the computational complexity theory as a NP-hard problem. In this …
is classified according to the computational complexity theory as a NP-hard problem. In this …
A sequential niche multimodal conformational sampling algorithm for protein structure prediction
Motivation Massive local minima on the protein energy landscape often cause traditional
conformational sampling algorithms to be easily trapped in local basin regions, because …
conformational sampling algorithms to be easily trapped in local basin regions, because …