Ten quick tips for homology modeling of high-resolution protein 3D structures.
The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational...
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Online Access: | https://doi.org/10.1371/journal.pcbi.1007449 |
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doaj-11438f68e1b24d1faa7b1e06f7ca902c2021-04-21T15:15:29ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-04-01164e100744910.1371/journal.pcbi.1007449Ten quick tips for homology modeling of high-resolution protein 3D structures.Yazan HaddadVojtech AdamZbynek HegerThe purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.https://doi.org/10.1371/journal.pcbi.1007449 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yazan Haddad Vojtech Adam Zbynek Heger |
spellingShingle |
Yazan Haddad Vojtech Adam Zbynek Heger Ten quick tips for homology modeling of high-resolution protein 3D structures. PLoS Computational Biology |
author_facet |
Yazan Haddad Vojtech Adam Zbynek Heger |
author_sort |
Yazan Haddad |
title |
Ten quick tips for homology modeling of high-resolution protein 3D structures. |
title_short |
Ten quick tips for homology modeling of high-resolution protein 3D structures. |
title_full |
Ten quick tips for homology modeling of high-resolution protein 3D structures. |
title_fullStr |
Ten quick tips for homology modeling of high-resolution protein 3D structures. |
title_full_unstemmed |
Ten quick tips for homology modeling of high-resolution protein 3D structures. |
title_sort |
ten quick tips for homology modeling of high-resolution protein 3d structures. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2020-04-01 |
description |
The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed. |
url |
https://doi.org/10.1371/journal.pcbi.1007449 |
work_keys_str_mv |
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