- Bioinfo tools
TP Atlas is a comprehensive "Targeted Proteins Research achievements database" in which you can access a variety of information on the target proteins, their structures, published papers and press release by navigating the network diagram drawn by Cell Illustrator for each TP Research project.
It covers all 35 TP projects ranging from signal transduction networks to enzymatic reaction pathways in the three fields of fundamental biology, medicine/pharmacology and food/environment.
(Cell Illustrator is a pathway drawing software developed by Prof. Satoru Miyano and his colleagues at the U.Tokyo)
AT Atlas will make you familiar with the accomplishments by research groups of "Protein Production", "Structural Analysis" and "Chemical Regulation" in the Targeted Proteins Research Program. AT Atlas is composed of graphical abstract (flow chart) , information in text including actual application of the method and link to PRotein Experimental Information Management System (PREIMS). You will be able to find experimental methods used to elucidate the structure and/or functions of proteins that you are interested in. Further, you will be able to reproduce the experimental process to study corresponding entries of PREIMS. (Most of the graphical abstracts have been drawn by use of Cell Illustrator that is a pathway-drawing software developed by Prof. Satoru Miyano and his colleagues at the U. Tokyo)
PREIMS is a database of various experimental protocols, which have been developed during the Target Proteins Research Project (TPRP). Researchers engaged in the TPRP submit their experimental protocols, which are viewed on this PREIMS portal with their accession priority.
The experimental protocols are described by ontology, constructed by the ontology editor, "Hozo", as well as by a normal flat text.
eSOL(Solubility database of all E.coli proteins) is a database on the solubility of entire ensemble E.coli proteins (Niwa T, Ying BW, Saito K, Jin W, Takada S, Ueda T and Taguchi H, 2009) individually synthesized by PURE system that is chaperon free.
To any user-specified protein the Functionally Annotated Japanese Protein Structural Information (FUJI) database expeditiously identifies various relevant data including structural information and displays them.
To any user-specified protein the Functionally Annotated Japanese Protein Structural Information (FUJI) database expeditiously identifies various relevant data including structural information and displays them. SNPs Mapping System is the extension of FUJI database and display the distribution of SNPs on 3D structure.
This new database for protein science was began to construct under the goal of
- collecting many kinds of protein related informations as many as possible from public databases all around the world,
- integrating these data, each of which is collected under the different purposes, into one unified database,
- as a result, constructing the next generation bioinformatic infrastructure for protein research field in Japan.
From three major public databases of amino acids, which are DDBJ DAD in Japan, NCBI NR in USA and UniRef in Europe, we already gathered over 21 million data of amino acids, over 53 million of species and over 112 million of cross-reference IDs. (updated on 16th February, 2011)
We started to compile a Protein-Compound Interaction Database (PCI DB) by collecting and merging information from dispersed databases with the aim of preparing information infrastructure for the next generation protein science.
The goal of the Autophagy Database is to provide up-to-date relevant information including protein structure data to researchers of autophagy, and to disseminate important findings to a wider audience so that their ramifications can be appreciated. For this purpose, we strive to make the database to contain as much pertinent information as possible and to make the contents freely available in a user-friendly format.
Enzymes that catalyze the biosynthesis of pyrimidine and the redox of protozoans are focused on as effective targets for drug development that can control trypanosomiasis, which is a fatal disease. This trypanosomes database system provides the comprehensive information for enzymes including candidate inhibitors and references.
|TAXONOMY ICON used by Trypanosomes DB is licensed under Creative Commons licenses.|
ToSY is an integrated computer program to predict a 3D structure of two proteins/domains in complex form.