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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Main Authors: Nimmanpipug P., Lee V.S., Chaijaruwanich J., Prasitwattanaseree S., Traisathit P.
Format: Conference or Workshop Item
Language:English
Published: 2014
Online Access: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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Institution: Chiang Mai University
Language: English
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spelling 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
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
language English
description 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
url 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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