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StructureProfiler: an all-in-one tool for 3D protein structure profiling
- Source :
- Bioinformatics (Oxford, England). 35(5)
- Publication Year :
- 2018
-
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. 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. 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. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
0303 health sciences
Protein function
Computer science
030302 biochemistry & molecular biology
Protein Data Bank (RCSB PDB)
Computational Biology
Proteins
computer.software_genre
Biochemistry
Computer Science Applications
03 medical and health sciences
Computational Mathematics
ComputingMethodologies_PATTERNRECOGNITION
Protein structure
Computational Theory and Mathematics
Drug Design
Profiling (information science)
Data mining
Molecular Biology
computer
Software
030304 developmental biology
Subjects
Details
- ISSN :
- 13674811
- Volume :
- 35
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- Bioinformatics (Oxford, England)
- Accession number :
- edsair.doi.dedup.....3076d19ee18f2b92d47a4e7a164eec4d