Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test
Attempts have been made to predict the binding structures of the human immunodeficiency virus-1 protease (HIV-1Pr) with various inhibitors within the shortest simulation time consuming. The purpose here is to improve the structural prediction by using statistical approach. We use a combination of mo...
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th-cmuir.6653943832-52092014-08-30T02:56:16Z Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test Nimmanpipug P. Lee V.S. Chaijaruwanich J. Prasitwattanaseree S. Traisathit P. Attempts have been made to predict the binding structures of the human immunodeficiency virus-1 protease (HIV-1Pr) with various inhibitors within the shortest simulation time consuming. The purpose here is to improve the structural prediction by using statistical approach. We use a combination of molecular docking and non-parametric binomial distribution test considering the combination of binding energy, hydrogen bonding, and hydrophobichydrophilic interaction in term of binding residues to select the most probable binding structure. In this study, the binding of HTV-1Pr and two inhibitors: Saquinavir and Litchi chinensis extracts (3-oxotrirucalla-7, 24-dien-21-oic acid) were investigated. Each inhibitor was positioned in the active site of HIV-1Pr in many different ways using Lamarckian genetic algorithm and then score each orientation by applying a reasonable evaluation function by AutoDock3.0 program. The results from search methods were screened out using nonparametric binomial distribution test and compared with the binding structure from explicit molecular dynamic simulation. Both complexes from statistical selected docking simulation were found to be comparable with those from X-ray diffraction analysis and explicit molecular dynamic simulation structures. © Springer-Verlag Berlin Heidelberg 2007. 2014-08-30T02:56:16Z 2014-08-30T02:56:16Z 2007 Conference Paper 3540712321; 9783540712329 03029743 69961 http://www.scopus.com/inward/record.url?eid=2-s2.0-34548057878&partnerID=40&md5=6bc3f6bd21a3a903023169b260c03ddb http://cmuir.cmu.ac.th/handle/6653943832/5209 English |
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Attempts have been made to predict the binding structures of the human immunodeficiency virus-1 protease (HIV-1Pr) with various inhibitors within the shortest simulation time consuming. The purpose here is to improve the structural prediction by using statistical approach. We use a combination of molecular docking and non-parametric binomial distribution test considering the combination of binding energy, hydrogen bonding, and hydrophobichydrophilic interaction in term of binding residues to select the most probable binding structure. In this study, the binding of HTV-1Pr and two inhibitors: Saquinavir and Litchi chinensis extracts (3-oxotrirucalla-7, 24-dien-21-oic acid) were investigated. Each inhibitor was positioned in the active site of HIV-1Pr in many different ways using Lamarckian genetic algorithm and then score each orientation by applying a reasonable evaluation function by AutoDock3.0 program. The results from search methods were screened out using nonparametric binomial distribution test and compared with the binding structure from explicit molecular dynamic simulation. Both complexes from statistical selected docking simulation were found to be comparable with those from X-ray diffraction analysis and explicit molecular dynamic simulation structures. © Springer-Verlag Berlin Heidelberg 2007. |
format |
Conference or Workshop Item |
author |
Nimmanpipug P. Lee V.S. Chaijaruwanich J. Prasitwattanaseree S. Traisathit P. |
spellingShingle |
Nimmanpipug P. Lee V.S. Chaijaruwanich J. Prasitwattanaseree S. Traisathit P. Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test |
author_facet |
Nimmanpipug P. Lee V.S. Chaijaruwanich J. Prasitwattanaseree S. Traisathit P. |
author_sort |
Nimmanpipug P. |
title |
Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test |
title_short |
Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test |
title_full |
Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test |
title_fullStr |
Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test |
title_full_unstemmed |
Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test |
title_sort |
structural screening of hiv-1 protease/inhibitor docking by non-parametric binomial distribution test |
publishDate |
2014 |
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http://www.scopus.com/inward/record.url?eid=2-s2.0-34548057878&partnerID=40&md5=6bc3f6bd21a3a903023169b260c03ddb http://cmuir.cmu.ac.th/handle/6653943832/5209 |
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1681420382027907072 |