Adaptive molecular docking method based on information entropy genetic algorithm

Li, Zhengfu; Gu, Junfeng; Zhuang, Hongyan; Kang, Ling; Wang, Guannan; Guo, Qizhong

doi:10.1016/j.asoc.2014.10.008

Cited by 52 publications

(32 citation statements)

References 28 publications

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“…Number of points in x, y and z were used respectively. All visualization of protein ligand interaction was evaluated using VMD software [42]. Cluster analysis was performed on the docked results using a root mean square deviation (RMSD) tolerance of 1.98 Å.…”

Section: Docking Proceduresmentioning

confidence: 99%

QSAR and Docking Study of Isatin Analogues as Cytotoxic Agents

Sabet

Khabnadideh

Fathi

et al. 2019

JPRI

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Computational chemistry is a unique method in the drug discovery process?? Explain Why?. In this study 109 molecules containing the isatin backbone were subjected to quantitative structure-activity relationship analysis to find the structure requirements for ligand binding. The structures were sketched and optimized in Hyperchem. The structural invariants used in this study were those obtained from whole molecular structures: by both hyperchem and dragon software (16 types of descriptors). Four chemometrics methods including MLR, FA-MLR, PCR and GA-PLS were employed to make connections between structural parameters and anticancer effects. MLR models revealed the effects of constitutional, functional, geometrical, WHIM and GETAWAY descriptors having higher impact on anticancer activity of the compounds. GA-PLS showed functional, constitutional and chemical descriptor indices to be the most significant parameters on anticancer activity. Moreover, the result of FA-MLR analysis revealed the effects of functional descriptors on the anticancer activity. A comparison between the different statistical methods employed and the results indicated that GA-PLS represented superior results and could explain and predict 81% and JPRI, 27(5): 1-22, 2019; Article no.JPRI.48076 2 78% variances in the PIC 50 data, respectively. Docking studies of these compounds were also investigated and promising results were obtained showing that some compounds were introduced as a good candidate for cancer agents. Original Research Article

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Section: Docking Proceduresmentioning

confidence: 99%

QSAR and Docking Study of Isatin Analogues as Cytotoxic Agents

Sabet

Khabnadideh

Fathi

et al. 2019

JPRI

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show abstract

“…To prepare the receptor structure, the three dimensional crystal structure of isatin (PDB:1Lx6) was acquired from Protein Data Bank (PDB data base; http://www.rcsb.org) [40] and water molecules and co-crystal ligand were removed from the structure. The PDB were then checked for missing atom types with the python script as implemented in MODELLER 9.17 [41]. The ligand structures were made by Hyper Chem software package (Version 7, Hypercube Inc).…”

Section: Data Screening and Model Buildingmentioning

confidence: 99%

QSAR, Docking Study of Isatin Analogues as Anti-bacterial Agents for Design New Compounds

Sabet

Jafroudi

2019

JPRI

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Computational chemistry is unique method in drug discovery which reduce cost. In this study 86 molecules containing isatin core were subjected to quantitative structure-activity relationship analysis and docking study to find the structure requirements for ligand binding. The structures were sketched and optimized in Hyperchem. The structural invariants used in this study were those obtained from whole molecular structures: by both hyperchem and dragon software (16 types of descriptors). Four chemometrics methods including MLR, FA-MLR, PCR and GA-PLS were employed to make connection between structural parameters and anticancer effects. MLR analysis explained the positive effect of the number of urea derivatives, thio urea, amide, thioamide, hydrazone, thiocarbohydrazone, nBnz with the halogen substitution on 5 position of isatin ring on the antimicrobial activity. It also shows nArCN, nPyridines have negative effects on the antimicrobial activity of studied compound. The FA-MLR describes the effect of 3D-MORSE and Galvez Topological charge descriptors and on antimicrobial activity of the studied compounds. The quality of PCRA equation is better than those derived from FA-MLR. A comparison between the different statistical methods employed revealed that GA-PLS represented superior results and it could explain and predict 73% and 68% of variances in the –LogMIC data, respectively. Comparison between QSAR and docking analysis revealed that by decreasing in number of ring and lipophilicity (also Logp) for design of new compounds can have better activity. Substitutions such as urea, thiourea, thiocarbohydrazone, benzhydrazide as on isatin ring, can cause better interaction with receptor.

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“…Soares and Knobbe studied entropy-based discretization methods for ranking data [21]. Li et al proposed a method to solve the problem of molecular docking using information entropy and the ant colony genetic algorithm [22]. Ma et al used information entropy to analyze the changes of substance in the processes of chemical changes [23].…”

Section: Related Workmentioning

confidence: 99%

A Novel Distance Metric: Generalized Relative Entropy

Liu

et al. 2017

Entropy

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Information entropy and its extension, which are important generalizations of entropy, are currently applied to many research domains. In this paper, a novel generalized relative entropy is constructed to avoid some defects of traditional relative entropy. We present the structure of generalized relative entropy after the discussion of defects in relative entropy. Moreover, some properties of the provided generalized relative entropy are presented and proved. The provided generalized relative entropy is proved to have a finite range and is a finite distance metric. Finally, we predict nucleosome positioning of fly and yeast based on generalized relative entropy and relative entropy respectively. The experimental results show that the properties of generalized relative entropy are better than relative entropy.Keywords: relative entropy; generalized relative entropy; upper bound; distance metric; adjusted distance BackgroundThe concept of entropy was proposed by T. Clausius as one of the parameters to reflect the degree of chaos for the object. Later, research found that information was such an abstract concept that was hard to make it clear to obtain its amount. Indeed, it was not until the information entropy was proposed by Shannon that we had a standard measure for the amount of information. Then, some related concepts based on information entropy have been proposed subsequently, such as cross entropy, relative entropy and mutual information, which offered an effective method to solve the complex problems of information processing. Therefore, the study of a novel metric based on information entropy was significant in the research domain of information science.Information entropy was first proposed by Shannon. Assuming an information source I is composed by n different signals I i , H(I), the information entropy of I was shown in Equation (1), where p i = amount of I i signal s amount of I denotes frequency of I i , E() means mathematical expectation, k > 1 denotes the base of logarithm. When k = 2, the unit of H(I) is bit.Information entropy was a metric of the chaos degree for an information source. The bigger the information entropy was, the more chaotic the information source, and vice versa. Afterwards cross entropy was proposed based on information entropy, the definition was shown in Equation (2) where P

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Adaptive molecular docking method based on information entropy genetic algorithm

Cited by 52 publications

References 28 publications

QSAR and Docking Study of Isatin Analogues as Cytotoxic Agents

QSAR and Docking Study of Isatin Analogues as Cytotoxic Agents

QSAR, Docking Study of Isatin Analogues as Anti-bacterial Agents for Design New Compounds

A Novel Distance Metric: Generalized Relative Entropy

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