3DinSight: An Integrated Database and Search Tool forStructure, Function and Property of Biomolecules

Jianghong An 1
ajh@rtc.riken.go.jp
Yasushi Kubota 2

Takao Nakama 2nakama@rtc.riken.go.jp
Akinori Sarai 1

kubota@rtc.riken.go.jp

sarai@rtc.riken.go.jp

1 Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN),
3-1-1 Koyadai, Tsukuba, Ibaraki, 305 Japan
2 Advanced Technology Institute Inc., 3-23-15 Jinbo, Kanda, Tokyo, 101 Japan

1 Introduction
In order to understand many biological phenomena, it is critical to get insight into the relationshipamong structure, function and property of biomolecules. However, it is usually dicult to infer therelation from individual data, since we usually need to examine several databases and literatures toobtain the necessary information. It would be useful to have an integrated database where one can
examine the relationship among structure, function and property. There are some services available
in the Internet to link various databases, but the relational information of biomolecular structure,function and property is rather scarce.
3DinSight is an integrated database, search and visualization tool for structure, function andproperty of biomolecules, developed to help researchers to get insight into their relationship [1]. Variouskinds of searches can be carried out though WWW interfaces. The locations of motif sequences andmutations are automatically mapped on the structure, and visualized by interactive viewers, VRML(Virtual Reality Modeling Language) and RasMol, where the mapped 3D objects are hyper-linked
to the corresponding document data. Also, the thermodynamic data of proteins and mutants areintegrated into 3DinSight. The amino-acid properties of a molecule, together with structural andfunctional information, can be displayed as a graph plot. 3DinSight is freely accessible through theInternet (http://www.rtc.riken.go.jp/3DinSight.html).

2 Relational database
We have implemented structural, functional and property data of biomolecules into SYBASE relational
database by creating various tables. The structural data are taken from PDB and daily updated. Those
data are also classi ed into several subsets according to sequence homology and functions.
As to the functional data, we have implemented PROSITE, which contains motifs of proteins.
The functional sites are mapped on amino-acid sequence and structure, and stored in a relational
table. We have also implemented the Protein Mutant Database (PMD), which contains a collection of
information about protein mutants. The mutant positions are mapped on the amino-acid sequencesof PDB by using the PDB-PIR cross-reference table. We created a table to relate the protein chainswith locations of mutations to make one-to-one correspondence to the location on structure.
We are developing Thermodynamic Database for Proteins and Mutants (ProTherm), which is acollection of various thermodynamic data of proteins and their mutants. Some of these data have direct
link to structural and functional information. Various properties of amino acids based on their physicochemical properties such as hydrophobicity and propensities for secondary structures are included as a328

table, by which one can examine the relationship among amino-acid property, structural and functionalinformation.
The present relational database also contains links to amino-acid databases, SWISS-PROT andPIR, where link information is updated according to the sequence homology. We are also developing
Protein-Nucleic Acid Recognition Database, which include structural database for protein-nucleic acidcomplex, base-amino acid interactions and prediction tools for transcription factor targets.

3 WWW interface
3DinSight can be accessed through the Internet by a WWW interface to the database. The addressof the main page is: http://www.rtc.riken.go.jp/3DinSight.html. One can combine various searches
such as entry, keywords, author, structure resolution and sequence pattern in the secondary structure,
for the speci ed dataset and display option linking functional information. 3DinSight also contains
various interfaces for searching PROSITE, Protein Mutant Database, PIR, SWISS-PROT, ProTherm
and Protein-Nucleic Acid Recognition Database. There are other convenient interfaces such as nding
motifs and sequence homologues in PDB for user's sequence. 3DinSight can also be searched by SQL
directly.
The screened structure and associated functional or mutation sites can be visualized by using visualization tools, VRML and RasMol [2]. In either case, structures can be displayed automatically by
selecting from the menu in the entry display, and the functional or mutation sites in the 3D structure
are clickable objects linked to the PROSITE or mutant documents, so that one can obtain the corresponding functional or mutational information such as description of the site and associated literature.
One can also do amino-acid analysis, where properties of the molecule can be examined; mathematical operations such as sum and average for each protein chain can be performed and displayed; theproperty pro les can be plotted and displayed as a graph, where the actual locations of secondarystructures, functional and mutation sites are automatically mapped.

References[1] An, J., Nakama, T., Kubota, Y., and Sarai, A., 3DinSight: An Integrated Relational Databaseand Search Tool for Structure, Function and Property of Biomolecules, Bioinformatics, 14:188{195, 1998.
[2] Nakama, T., An, J., Kubota, Y., and Sarai, A. Visualization of Functional Sites on Protein
Structures by Virtual Reality Modeling Language, Bioimages, 5:59{64, 1997.

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