Publication detail

Ten quick tips for homology modeling of high-resolution protein 3D structures

HADDAD, Y. ADAM, V. HEGER, Z.

Original Title

Ten quick tips for homology modeling of high-resolution protein 3D structures

Type

journal article in Web of Science

Language

English

Original Abstract

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.

Keywords

protein 3D structures; repositories; homology modeling; molecular docking and molecular dynamics

Authors

HADDAD, Y.; ADAM, V.; HEGER, Z.

Released

30. 4. 2020

Publisher

PLOS

ISBN

1553-734X

Periodical

PLoS Computational Biology

Year of study

16

Number

4

State

United States of America

Pages from

1

Pages to

19

Pages count

19

URL

https://doi.org/10.1371/journal.pcbi.1007449

Full text in the Digital Library

http://hdl.handle.net/11012/188175

BibTex

@article{BUT164134,
  author="Yazan Abdulmajeed Eyadh {Haddad} and Vojtěch {Adam} and Zbyněk {Heger}",
  title="Ten quick tips for homology modeling of high-resolution protein 3D structures",
  journal="PLoS Computational Biology",
  year="2020",
  volume="16",
  number="4",
  pages="1--19",
  doi="10.1371/journal.pcbi.1007449",
  issn="1553-734X",
  url="https://doi.org/10.1371/journal.pcbi.1007449"
}