Back to Search Start Over

StructureProfiler: an all-in-one tool for 3D protein structure profiling.

StructureProfiler: an all-in-one tool for 3D protein structure profiling.

Authors :
Meyder A
Kampen S
Sieg J
Fährrolfes R
Friedrich NO
Flachsenberg F
Rarey M
Source :
Bioinformatics (Oxford, England) [Bioinformatics] 2019 Mar 01; Vol. 35 (5), pp. 874-876.
Publication Year :
2019

Abstract

Motivation: Three-dimensional protein structures are important starting points for elucidating protein function and applications like drug design. Computational methods in this area rely on high quality validation datasets which are usually manually assembled. Due to the increase in published structures as well as the increasing demand for specially tailored validation datasets, automatic procedures should be adopted.<br />Results: StructureProfiler is a new tool for automatic, objective and customizable profiling of X-ray protein structures based on the most frequently applied selection criteria currently in use to assemble benchmark datasets. As examples, four dataset configurations (Astex, Iridium, Platinum, combined), all results of the combined tests and the list of all PDB Ids passing the combined criteria set are attached in the Supplementary Material.<br />Availability and Implementation: StructureProfiler is available as part of the ProteinsPlus web service http://proteins.plus and as standalone tool in the NAOMI ChemBio Suite. Dataset updates together with the tool can be found on http://www.zbh.uni-hamburg.de/structureprofiler.<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Details

Language :
English
ISSN :
1367-4811
Volume :
35
Issue :
5
Database :
MEDLINE
Journal :
Bioinformatics (Oxford, England)
Publication Type :
Academic Journal
Accession number :
30124779
Full Text :
https://doi.org/10.1093/bioinformatics/bty692