PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, Andre Leier, Jerico Revote, Cangzhi Jia, Yan Zhu, A. Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites’ data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence–structural–functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu.ezproxy.lib.monash.edu.au/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.
Original languageEnglish
Article numberbbz050
Number of pages11
JournalBriefings in Bioinformatics
DOIs
Publication statusAccepted/In press - 4 Jun 2019

Keywords

  • post-translational modifications
  • mutation
  • functional impact
  • database
  • bioinformatics

Cite this

@article{9e7818af069046b0ab173b1b253c2a32,
title = "PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact",
abstract = "Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites’ data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence–structural–functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu.ezproxy.lib.monash.edu.au/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.",
keywords = "post-translational modifications, mutation, functional impact, database, bioinformatics",
author = "Fuyi Li and Cunshuo Fan and Marquez-Lago, {Tatiana T.} and Andre Leier and Jerico Revote and Cangzhi Jia and Yan Zhu and Smith, {A. Ian} and Webb, {Geoffrey I.} and Quanzhong Liu and Leyi Wei and Jian Li and Jiangning Song",
year = "2019",
month = "6",
day = "4",
doi = "10.1093/bib/bbz050",
language = "English",
journal = "Briefings in Bioinformatics",
issn = "1467-5463",
publisher = "Oxford Univ Press",

}

PRISMOID : a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. / Li, Fuyi; Fan, Cunshuo; Marquez-Lago, Tatiana T.; Leier, Andre; Revote, Jerico; Jia, Cangzhi ; Zhu, Yan; Smith, A. Ian; Webb, Geoffrey I.; Liu, Quanzhong; Wei, Leyi; Li, Jian; Song, Jiangning.

In: Briefings in Bioinformatics, 04.06.2019.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - PRISMOID

T2 - a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

AU - Li, Fuyi

AU - Fan, Cunshuo

AU - Marquez-Lago, Tatiana T.

AU - Leier, Andre

AU - Revote, Jerico

AU - Jia, Cangzhi

AU - Zhu, Yan

AU - Smith, A. Ian

AU - Webb, Geoffrey I.

AU - Liu, Quanzhong

AU - Wei, Leyi

AU - Li, Jian

AU - Song, Jiangning

PY - 2019/6/4

Y1 - 2019/6/4

N2 - Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites’ data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence–structural–functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu.ezproxy.lib.monash.edu.au/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.

AB - Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites’ data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence–structural–functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu.ezproxy.lib.monash.edu.au/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.

KW - post-translational modifications

KW - mutation

KW - functional impact

KW - database

KW - bioinformatics

U2 - 10.1093/bib/bbz050

DO - 10.1093/bib/bbz050

M3 - Article

JO - Briefings in Bioinformatics

JF - Briefings in Bioinformatics

SN - 1467-5463

M1 - bbz050

ER -