PDB-tools web: A user-friendly interface for the manipulation of PDB files

被引：16

作者：

Jimenez-Garcia, Brian ^{[1
]}

Teixeira, Joao M. C. ^{[2
]}

Trellet, Mikael ^{[1
]}

Rodrigues, Joao P. G. L. M. ^{[3
]}

Bonvin, Alexandre M. J. J. ^{[1
]}

机构：

[1] Univ Utrecht, Bijvoet Ctr Biomol Res, NL-3584 CH Utrecht, Netherlands

[2] Hosp Sick Children, Program Mol Med, Toronto, ON, Canada

[3] Stanford Univ, Dept Struct Biol, Sch Med, Stanford, CA 94305 USA

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2021年 / 89卷 / 03期

基金：

欧盟地平线“2020”; 美国国家卫生研究院;

关键词：

bioinformatics; PDB; structural biology; web server; VISUALIZATION; DISVIS; SERVER; PARSER;

D O I：

10.1002/prot.26018

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Protein Data Bank (PDB) file format remains a popular format used and supported by many software to represent coordinates of macromolecular structures. It however suffers from drawbacks such as error-prone manual editing. Because of that, various software toolkits have been developed to facilitate its editing and manipulation, but, to date, there is no online tool available for this purpose. Here we present PDB-Tools Web, a flexible online service for manipulating PDB files. It offers a rich and user-friendly graphical user interface that allows users to mix-and-match more than 40 individual tools from the pdb-tools suite. Those can be combined in a few clicks to perform complex pipelines, which can be saved and uploaded. The resulting processed PDB files can be visualized online and downloaded. The web server is freely available at .

引用

页码：330 / 335

页数：6

共 50 条

[1] User-friendly interface for fast and easy construction of Dalton input files
Karin Holk
Andreas L. Vishart
Kurt V. Mikkelsen
Journal of Molecular Modeling, 2020, 26
[2] User-friendly interface for fast and easy construction of Dalton input files
Holk, Karin
Vishart, Andreas L.
Mikkelsen, Kurt, V
JOURNAL OF MOLECULAR MODELING, 2020, 26 (10)
[3] PRIDEViewer: A novel user-friendly interface to visualize PRIDE XML files
Alberto Medina-Aunon, J.
Carazo, Jose M.
Pablo Albar, Juan
PROTEOMICS, 2011, 11 (02) : 334 - 337
[4] PDB Editor: a user-friendly Java']Java-based Protein Data Bank file editor with a GUI
Lee, Jonas
Kim, Sung-Hou
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2009, 65 : 399 - 402
[5] Nonverbal interface for user-friendly manipulation based on natural motion
Sato, E
Nakajima, A
Yamaguchi, T
2005 IEEE International Symposium on Computational Intelligence in Robotics and Automation, Proceedings, 2005, : 499 - 504
[6] TRIANGLE Portal: An User-Friendly Web Interface for Remote Experimentation
Diaz-Zayas, Almudena
Salmeron Moreno, Alberto
Garcia Pascual, Gustavo
Merino Gomez, Pedro
SMART INDUSTRY & SMART EDUCATION, 2019, 47 : 110 - 117
[7] User-friendly text on the web
Jacobsen, Jens
i-com, 2006, 5 (01) : 72 - 74
[8] A USER-FRIENDLY INTERFACE ADAPTER
BOWEN, J
MICROPROCESSORS AND MICROSYSTEMS, 1985, 9 (09) : 432 - 439
[9] rbioapi: user-friendly R interface to biologic web services' API
Rezwani, Moosa
Pourfathollah, Ali Akbar
Noorbakhsh, Farshid
BIOINFORMATICS, 2022, 38 (10) : 2952 - 2953
[10] EasyModel: a user-friendly web-based interface based on MODELLER
Seyed Shahriar Arab
Alireza Dantism
Scientific Reports, 13 (1)

← 1 2 3 4 5 →