Protocol for protein structure modelling

Amara Jabeen; Abidali Mohamedali; Shoba Ranganathan

doi:10.1016/B978-0-12-809633-8.20477-9

Protocol for protein structure modelling

Amara Jabeen, Abidali Mohamedali, Shoba Ranganathan

Research output: Chapter in Book/Report/Conference proceeding › Entry for encyclopedia/dictionary/reference book

16 Citations (Scopus)

Abstract

In silico protein structure prediction methods are assisting the field of structural biology by complementing expensive and laborious experimental methods. During the past few decades, improvements in computational techniques have achieved significant developments in protein structure prediction methods, of which template-based methods have the highest accuracy. This article presents a comprehensive protocol for modelling 3-dimensional (3D) structures of proteins from identified structural templates. The 3D model generated is also screened for functional motifs and patterns so that the selected structural model represents a functional protein. The article concludes by presenting the suite of available structure modelling tools and automated webservers for protein structure prediction to assist readers in elucidating the most appropriate choice for their purpose according to the problem scenario.

Original language	English
Title of host publication	Encyclopedia of bioinformatics and computational biology
Subtitle of host publication	ABC of Bioinformatics
Editors	Mario Cannataro, Bruno Gaeta, Mohammad Asif Khan
Place of Publication	Amsterdam; Oxford; Cambridge
Publisher	Elsevier
Pages	252-272
Number of pages	21
Volume	3
ISBN (Electronic)	9780128114322
ISBN (Print)	9780128114148
DOIs	https://doi.org/10.1016/B978-0-12-809633-8.20477-9
Publication status	Published - 2019

Bibliographical note

Editors-in-chief: Shoba Ranganathan, Kenta Nakai, Christian Schönbach, Michael Gribskov.

Keywords

Bioinformatics tools
Homology modelling
Motifs and patterns
Profile alignment
Protein structure predictions
Protein structure validation
Sequence analysis
Sequence structure alignment
Tertiary structure
Transmembrane helices

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10.1016/B978-0-12-809633-8.20477-9

Cite this

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abstract = "In silico protein structure prediction methods are assisting the field of structural biology by complementing expensive and laborious experimental methods. During the past few decades, improvements in computational techniques have achieved significant developments in protein structure prediction methods, of which template-based methods have the highest accuracy. This article presents a comprehensive protocol for modelling 3-dimensional (3D) structures of proteins from identified structural templates. The 3D model generated is also screened for functional motifs and patterns so that the selected structural model represents a functional protein. The article concludes by presenting the suite of available structure modelling tools and automated webservers for protein structure prediction to assist readers in elucidating the most appropriate choice for their purpose according to the problem scenario.",

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Protocol for protein structure modelling. / Jabeen, Amara ; Mohamedali, Abidali ; Ranganathan, Shoba.
Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics. ed. / Mario Cannataro; Bruno Gaeta; Mohammad Asif Khan. Vol. 3 Amsterdam; Oxford; Cambridge: Elsevier, 2019. p. 252-272.

Research output: Chapter in Book/Report/Conference proceeding › Entry for encyclopedia/dictionary/reference book

TY - CHAP

T1 - Protocol for protein structure modelling

AU - Jabeen, Amara

AU - Mohamedali, Abidali

AU - Ranganathan, Shoba

N1 - Editors-in-chief: Shoba Ranganathan, Kenta Nakai, Christian Schönbach, Michael Gribskov.

PY - 2019

Y1 - 2019

N2 - In silico protein structure prediction methods are assisting the field of structural biology by complementing expensive and laborious experimental methods. During the past few decades, improvements in computational techniques have achieved significant developments in protein structure prediction methods, of which template-based methods have the highest accuracy. This article presents a comprehensive protocol for modelling 3-dimensional (3D) structures of proteins from identified structural templates. The 3D model generated is also screened for functional motifs and patterns so that the selected structural model represents a functional protein. The article concludes by presenting the suite of available structure modelling tools and automated webservers for protein structure prediction to assist readers in elucidating the most appropriate choice for their purpose according to the problem scenario.

AB - In silico protein structure prediction methods are assisting the field of structural biology by complementing expensive and laborious experimental methods. During the past few decades, improvements in computational techniques have achieved significant developments in protein structure prediction methods, of which template-based methods have the highest accuracy. This article presents a comprehensive protocol for modelling 3-dimensional (3D) structures of proteins from identified structural templates. The 3D model generated is also screened for functional motifs and patterns so that the selected structural model represents a functional protein. The article concludes by presenting the suite of available structure modelling tools and automated webservers for protein structure prediction to assist readers in elucidating the most appropriate choice for their purpose according to the problem scenario.

KW - Bioinformatics tools

KW - Homology modelling

KW - Motifs and patterns

KW - Profile alignment

KW - Protein structure predictions

KW - Protein structure validation

KW - Sequence analysis

KW - Sequence structure alignment

KW - Tertiary structure

KW - Transmembrane helices

UR - https://www.scopus.com/pages/publications/85059757018

U2 - 10.1016/B978-0-12-809633-8.20477-9

DO - 10.1016/B978-0-12-809633-8.20477-9

M3 - Entry for encyclopedia/dictionary/reference book

AN - SCOPUS:85059757018

SN - 9780128114148

VL - 3

SP - 252

EP - 272

BT - Encyclopedia of bioinformatics and computational biology

A2 - Cannataro, Mario

A2 - Gaeta, Bruno

A2 - Asif Khan, Mohammad

PB - Elsevier

CY - Amsterdam; Oxford; Cambridge

ER -

Protocol for protein structure modelling

Abstract

Bibliographical note

Keywords

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