MEDALS METI Life science integrated database portal site

ProSeg

Summary	ProSeg is a database of local structures of protein segments. ProSeg contains thousands of clusters of protein segments that were classified according to their three-dimensional structural resemblance.
Data type	Protein-motif

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Rat Brain Sections

Summary	This database provides whole section images of rat brain recorded in ultra high resolution. You can see each neuron if you zoom in the images. The database was created by AIST, Eizou Bijutsuin, and PFU Limited.(cited from the original site)
Data type	Morphology image

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SARS(severe acute respiratory syndrome)-CoV2 Protein NMR Database

Summary	As part of the AMED project "Project for Developing Technologies for Addressing the Novel Coronavirus Disease and Other Infectious Diseases", Cellular and Molecular Bioengineering Research Institute @AIST have successfully expressed and purified 27 of the 45 structural domains in the SARS-CoV-2 proteins, using a cell-free expression system. These cover more than 50% of ORF in the virus. We also succeeded to obtain atypical proteins such as ORF3b and ORF9b
Data type	NMR spectra

Summary

As part of the AMED project "Project for Developing Technologies for Addressing the Novel Coronavirus Disease and Other Infectious Diseases", Cellular and Molecular Bioengineering Research Institute @AIST have successfully expressed and purified 27 of the 45 structural domains in the SARS-CoV-2 proteins, using a cell-free expression system. These cover more than 50% of ORF in the virus. We also succeeded to obtain atypical proteins such as ORF3b and ORF9b

Data type

NMR spectra

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SEVENS

Summary	SEVENS database includes G-protein coupled receptors (GPCR) genes with seven transmembrane helices, that are identified with high accuracy from complete genomes of 32 eukaryotes, by a pipeline integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a TMH predictor.
Data type	Ptotein-sequence amino acid sequence

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TMBETA-DISC

Summary	We have developed statistical and SVM based methods for discriminating beta barrel membrane proteins from amino acid sequence. The amino acid composition, residue pair preference and motifs are the major attributes for the program. 5 programs (TMBETADISC-COMP, TMBETADISC-DIPEPTIDE, TMBETADISC-MOTIF, TMBETADISC-SVM, TMBETADISC-RBF) was included in TMBETADISC (cited from the original site).
Data type	Protein-AminoAcid

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TMBETA-GENOME

Summary	TMBETA-GENOME is a collection of amino acid sequences for all the completed genomes and the "annotated beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. Web interfaces to discriminate beta-barrel membrane proteins have been provided from this cite( ""TMBETA-DISC"" and ""TMBETA-SVM"")."
Data type	Protein-structure

Summary

TMBETA-GENOME is a collection of amino acid sequences for all the completed genomes and the "annotated beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. Web interfaces to discriminate beta-barrel membrane proteins have been provided from this cite( ""TMBETA-DISC"" and ""TMBETA-SVM"")."

Data type

Protein-structure

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TMFunction

Summary	TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins (cited from the original site).
Data type	Protein-structure ,　functional residues

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TOT-DB

Summary	TOT-DB (The Theileria orientalis Genome Annotation Database) ia a database of the genome information of parasitic protists Theileria orientalis.Genes annotated by an integration of expression data and gene prediction by several software are displayed on the G-integra genome browser.TOT-DB also offers the BLAST homolgy search service and data downloads of the genome sequences and gene annotation of T. orientalis.
Data type	Comparative genomics

Summary

TOT-DB (The Theileria orientalis Genome Annotation Database) ia a database of the genome information of parasitic protists Theileria orientalis.Genes annotated by an integration of expression data and gene prediction by several software are displayed on the G-integra genome browser.TOT-DB also offers the BLAST homolgy search service and data downloads of the genome sequences and gene annotation of T. orientalis.

Data type

Comparative genomics

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TraP

Summary	The metabolic pathways were compared, such as glycolysis, the TCA cycle, amino acid biosynthesis, and nucleic acid biosynthesis among 7 archaea. It is possible to highlight the differences between different archaea. (cited from the original site)
Data type	Metabolite repression

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VarySysDB

Summary	This is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. It provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains.
Data type	-

Summary

This is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. It provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains.

Data type

-

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