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GTOP specifications


Unique identifier OMICS_21106
Alternative name Genomes TO Protein Structures and Functions database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Publications for Genomes TO Protein Structures and Functions database

GTOP citations


Yeast Sub1 and human PC4 are G quadruplex binding proteins that suppress genome instability at co transcriptionally formed G4 DNA

Nucleic Acids Res
PMCID: 5449603
PMID: 28369605
DOI: 10.1093/nar/gkx201

[…] -3΄) (,). In order to determine whether Sub1 also binds to G4 DNA formed by the Ig switch Mu sequence integrated into the recombination reporter constructs used in the genetic assays above (pTET-lys2-GTOP and –GBTM), we first performed circular dichroism (CD) analysis with a 45-mer oligonucleotide partially representing this sequence (SμG; ). The CD spectrum with a shallow minimum at ∼240 nm and a […]


Prediction of Protein Destabilizing Polymorphisms by Manual Curation with Protein Structure

PLoS One
PMCID: 3506574
PMID: 23189203
DOI: 10.1371/journal.pone.0050445
call_split See protocol

[…] ated for sample cDNAs in and . A link to a CHIME 3D image of each structure to which all or part of the cDNA was aligned is included in this web page (). All 3D images herein were prepared using the GTOP system and the CHIME plug-in, except for those of , which were prepared with the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of Cali […]


Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron 5 of the Sheep SCF Gene: A Novel Splice Variant

PLoS One
PMCID: 3376141
PMID: 22719917
DOI: 10.1371/journal.pone.0038657

[…] orkspace v 8.0.5 , Reverse PSI-BLAST (in BLAST 2.2.12 packages) search against protein data bank (PDB) and Structural Classification of Proteins (SCOP) at Genomes TO Protein structures and functions (GTOP) .The homology modeling was performed with Modeller 9v2 using an integrated multiple sequence alignment and multiple structure visualization application ‘Friend’ v. 2.0 . All the modelled struct […]


Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors

BMC Struct Biol
PMCID: 2687452
PMID: 19402914
DOI: 10.1186/1472-6807-9-26

[…] I-BLAST searches against the PDB (Apr. 6, 2007 version) and SCOP [] (version 1.69) and HMMER searches against SCOP. Because the assignments of structural domains above are conducted and stored in the GTOP database[,] in a genome-wide scale, we took analyzed data, including DISOPRED2 prediction [], from GTOP. Trans-membrane (TM) regions were assigned according to the Swiss-Prot annotations, and the […]


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GTOP institution(s)
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Shizuoka, Japan; HOLONICS Corporation, Shizuoka, Japan; Department of Bioinformatics, Maebashi Institute of Technology, Gunma, Japan
GTOP funding source(s)
Supported by the Target Protein Research Program from the Ministry of Education, Culture, Sports, Science and Technology of Japan; and by the Bioinformatics Research and Development Project from the Japan Science and Technology Agency.

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