PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design

The shortest path problem is one of the optimization problems where the optimization value is a distance. In general, solving the problem of the shortest route search can be done using two methods, namely conventional methods and heuristic methods. The Ant Colony Optimization (ACO) is the one of the optimization algorithm based on heuristic method. ACO is adopted from the behavior of ant colonies which naturally able to find the shortest route on the way from the nest to the food sources. In this study, ACO is used to determine the shortest route from Bumi Senyiur Hotel (origin point) to East Kalimantan Governor's Office (destination point). The selection of the origin and destination points is based on a large number of possible major roads connecting the two points. The data source used is the base map of Samarinda City which is cropped on certain coordinates by using Google Earth app which covers the origin and destination points selected. The data pre-processing is performed on the base map image of the acquisition results to obtain its numerical data. ACO is implemented on the data to obtain the shortest path from the origin and destination point that has been determined. From the study results obtained that the number of ants that have been used has an effect on the increase of possible solutions to optimal. The number of tours effect on the number of pheromones that are left on each edge passed ant. With the global pheromone update on each tour then there is a possibility that the path that has passed the ant will run out of pheromone at the end of the tour. This causes the possibility of inconsistent results when using the number of ants smaller than the number of tours.

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Modeling and optimizing logistics, information, economic and financial intercluster cooperation using the ant colony optimization algorithm

Finance and Credit ◽

10.24891/fc.26.11.2427 ◽

2020 ◽

Vol 26 (11) ◽

pp. 2427-2447

Author(s):

S.N. Yashin ◽

E.V. Koshelev ◽

S.A. Borisov

Keyword(s):

Ant Colony Optimization ◽

Optimization Algorithm ◽

Population Decline ◽

Innovation System ◽

Federal District ◽

Original Model ◽

Ant Colony ◽

Industrial Agglomeration ◽

Ant Colony Optimization Algorithm

Subject. This article discusses the issues related to the creation of a technology of modeling and optimization of economic, financial, information, and logistics cluster-cluster cooperation within a federal district. Objectives. The article aims to propose a model for determining the optimal center of industrial agglomeration for innovation and industry clusters located in a federal district. Methods. For the study, we used the ant colony optimization algorithm. Results. The article proposes an original model of cluster-cluster cooperation, showing the best version of industrial agglomeration, the cities of Samara, Ulyanovsk, and Dimitrovgrad, for the Volga Federal District as a case study. Conclusions. If the industrial agglomeration center is located in these three cities, the cutting of the overall transportation costs and natural population decline in the Volga Federal District will make it possible to qualitatively improve the foresight of evolution of the large innovation system of the district under study.

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A Hybrid Intrusion Detection System Using Hypper-Pipe Classifier and Ant Colony Optimization

International Journal of Computer Sciences and Engineering ◽

10.26438/ijcse/v6i11.376380 ◽

2018 ◽

Vol 6 (11) ◽

pp. 376-380

Author(s):

K Shukla ◽

R K Gupta ◽

V. Namdeo

Keyword(s):

Intrusion Detection ◽

Ant Colony Optimization ◽

Intrusion Detection System ◽

Detection System ◽

Ant Colony

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Improving the Accuracy of Protein-Ligand Binding Affinity Prediction by Deep Learning Models: Benchmark and Model

10.26434/chemrxiv.9866912 ◽

2019 ◽

Author(s):

Mohammad Rezaei ◽

Yanjun Li ◽

Xiaolin Li ◽

Chenglong Li

Keyword(s):

Deep Learning ◽

Drug Design ◽

Binding Affinity ◽

Benchmark Dataset ◽

Rational Drug Design ◽

Learning Models ◽

Structure Based Drug Design ◽

Binding Affinity Prediction ◽

Affinity Prediction ◽

Rational Drug

Introduction: The ability to discriminate among ligands binding to the same protein target in terms of their relative binding affinity lies at the heart of structure-based drug design. Any improvement in the accuracy and reliability of binding affinity prediction methods decreases the discrepancy between experimental and computational results. Objectives: The primary objectives were to find the most relevant features affecting binding affinity prediction, least use of manual feature engineering, and improving the reliability of binding affinity prediction using efficient deep learning models by tuning the model hyperparameters. Methods: The binding site of target proteins was represented as a grid box around their bound ligand. Both binary and distance-dependent occupancies were examined for how an atom affects its neighbor voxels in this grid. A combination of different features including ANOLEA, ligand elements, and Arpeggio atom types were used to represent the input. An efficient convolutional neural network (CNN) architecture, DeepAtom, was developed, trained and tested on the PDBbind v2016 dataset. Additionally an extended benchmark dataset was compiled to train and evaluate the models. Results: The best DeepAtom model showed an improved accuracy in the binding affinity prediction on PDBbind core subset (Pearson’s R=0.83) and is better than the recent state-of-the-art models in this field. In addition when the DeepAtom model was trained on our proposed benchmark dataset, it yields higher correlation compared to the baseline which confirms the value of our model. Conclusions: The promising results for the predicted binding affinities is expected to pave the way for embedding deep learning models in virtual screening and rational drug design fields.

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