Bilinear optimization of protein structure prediction: An exact approach via AB off-lattice model

LSA da Silva, LO Seman, E Camponogara… - Computers in biology …, 2024 - Elsevier
Protein structure prediction (PSP) remains a central challenge in computational biology due
to its inherent complexity and high dimensionality. While numerous heuristic approaches …

Inverse design of nanophotonic devices using generative adversarial networks

W Kim, S Kim, M Lee, J Seok - Engineering Applications of Artificial …, 2022 - Elsevier
The efficient design of structures that exhibit desired properties is challenging across various
engineering and scientific applications. Traditional methods employ experts in a specific …

On the role of metaheuristic optimization in bioinformatics

L Calvet, S Benito, AA Juan… - … in Operational Research, 2023 - Wiley Online Library
Metaheuristic algorithms are employed to solve complex and large‐scale optimization
problems in many different fields, from transportation and smart cities to finance. This paper …

Adoption of an improved PSO to explore a compound multi-objective energy function in protein structure prediction

S Song, J Ji, X Chen, S Gao, Z Tang, Y Todo - Applied Soft Computing, 2018 - Elsevier
The protein structure prediction (PSP) problem, ie, predicting the three-dimensional structure
of a protein from its sequence, remains challenging in computational biology. The …

Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model

L Zhang, H Ma, W Qian, H Li - Computational Biology and Chemistry, 2020 - Elsevier
This paper proposed an improved simulated annealing (ISA) algorithm for protein structure
optimization based on a three-dimensional AB off-lattice model. In the algorithm, we …

Protein folding optimization using differential evolution extended with local search and component reinitialization

B Bošković, J Brest - Information Sciences, 2018 - Elsevier
This paper presents a novel Differential Evolution algorithm for protein folding optimization
that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes …

Fractional-order modeling and fuzzy clustering of improved artificial bee colony algorithms

S Zhou, X Xu, Z Xu, W Chang… - IEEE transactions on …, 2019 - ieeexplore.ieee.org
This article proposes an improved artificial bee colony algorithm (IABC) for maintaining a
balance between the exploratory and exploitative abilities of the algorithm. Therefore …

A GPU-based hybrid jDE algorithm applied to the 3D-AB protein structure prediction

M Boiani, RS Parpinelli - Swarm and Evolutionary Computation, 2020 - Elsevier
Abstract The Protein Structure Prediction (PSP) problem is one of the most significant open
problems in bioinformatics. In the AB off-lattice model, the protein sequence is labeled as …

Selection of appropriate metaheuristic algorithms for protein structure prediction in AB off-lattice model: a perspective from fitness landscape analysis

ND Jana, J Sil, S Das - Information Sciences, 2017 - Elsevier
Protein structure prediction (PSP) from its primary sequence is a challenging task in
computational biology. PSP is an optimization problem that determines the stable or native …

Chaotic variants of grasshopper optimization algorithm and their application to protein structure prediction

A Saxena, R Kumar - Applied nature-inspired computing: Algorithms and …, 2020 - Springer
It is a known fact that protein structure prediction is a challenging problem of computational
biology. In the past, several attempts of application of metaheuristic approaches have been …