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...

Full description

Saved in:
Bibliographic Details
Main Authors: Piyarat Nimmanpipug, Vannajan Sanghiran Lee, Jeerayut Chaijaruwanich, Sukon Prasitwattanaseree, Patrinee Traisathit
Format: Conference Proceeding
Published: 2018
Subjects:
Online Access:https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=34548057878&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/60985
Tags: Add Tag
No Tags, Be the first to tag this record!
Institution: Chiang Mai University
id th-cmuir.6653943832-60985
record_format dspace
spelling th-cmuir.6653943832-609852018-09-10T04:06:49Z Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test Piyarat Nimmanpipug Vannajan Sanghiran Lee Jeerayut Chaijaruwanich Sukon Prasitwattanaseree Patrinee Traisathit Computer Science Mathematics 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. 2018-09-10T04:02:26Z 2018-09-10T04:02:26Z 2007-08-27 Conference Proceeding 16113349 03029743 2-s2.0-34548057878 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=34548057878&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/60985
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Computer Science
Mathematics
spellingShingle Computer Science
Mathematics
Piyarat Nimmanpipug
Vannajan Sanghiran Lee
Jeerayut Chaijaruwanich
Sukon Prasitwattanaseree
Patrinee Traisathit
Structural screening of HIV-1 protease/inhibitor docking by non-parametric binomial distribution test
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 Proceeding
author Piyarat Nimmanpipug
Vannajan Sanghiran Lee
Jeerayut Chaijaruwanich
Sukon Prasitwattanaseree
Patrinee Traisathit
author_facet Piyarat Nimmanpipug
Vannajan Sanghiran Lee
Jeerayut Chaijaruwanich
Sukon Prasitwattanaseree
Patrinee Traisathit
author_sort Piyarat Nimmanpipug
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 2018
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=34548057878&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/60985
_version_ 1681425537062404096