Dataset Information

AngioDB: database of angiogenesis and angiogenesis-related molecules.

ABSTRACT: Angiogenesis is the formation of new capillaries sprouting from pre-existing vessels. Angiogenesis occurs in a variety of normal physiological and pathological conditions and is regulated by a balance of stimulatory and inhibitory angiogenic factors. The control of this balance may fail and result in the formation of a pathologic capillary network during the development of many diseases. Therefore, we developed the angiogenesis database (AngioDB), which can provide a signaling network of angiogenesis-related biomolecules in human. Each record of AngioDB consisted of 12 fields and was developed by using a relational database management system. For the retrieval of data, Active Server Page (ASP) technology was integrated in this system. Users can access the database by a query or imagemap browsing program. The retrieving system also provides a list of angiogenesis-related molecules classified by three categories, and the database has an external link to NCBI databases. AngioDB is available via the Internet at http://angiodb.snu.ac.kr/.

SUBMITTER: Sohn TK

PROVIDER: S-EPMC99150 | biostudies-literature | 2002 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

AngioDB: database of angiogenesis and angiogenesis-related molecules.

Sohn Tae-Kwon TK Moon Eun-Joung EJ Lee Seok-Ki SK Cho Hwan-Gue HG Kim Kyu-Won KW

Nucleic acids research 20020101 1

Angiogenesis is the formation of new capillaries sprouting from pre-existing vessels. Angiogenesis occurs in a variety of normal physiological and pathological conditions and is regulated by a balance of stimulatory and inhibitory angiogenic factors. The control of this balance may fail and result in the formation of a pathologic capillary network during the development of many diseases. Therefore, we developed the angiogenesis database (AngioDB), which can provide a signaling network of angioge ...[more]

PMID: 11752339

Similar Datasets

Project description:BACKGROUND:Interactions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high resolution structures. Although knowledge accumulated on a case-by-case basis is valuable, it is also important to study the ion-protein interaction statistically. From experimentally determined structures, it is possible to examine the ion distribution around each amino acid. Such distributions can reveal relation between ions and amino acids, so it is desirable to carry out a systematic survey of 'ion-amino acid' pairing interaction and share the information with a publicly available database. RESULTS:The survey in the Protein Data Bank (PDB) revealed that approximately 40% of molecules records contain at least one ion. To reduce the bias resulted from protein redundancy, the statistics were extracted from a non-redundant dataset by excluding the proteins with similar sequences. Based on the structures of protein molecules and the location of ions, the statistical distributions of ions around each proteinogenic amino acid type were investigated and further summarized in a database. To systematically quantify the interactions between ions and each amino acid, the positions of ions were mapped to the coordinate system centered at each neighboring amino acid. It was found that the distribution of ions follows the expected rules governed by the physicochemical interactions in general. Large variations were observed, reflecting the preference in 'ion-amino acid' interactions. The analysis program is written in the Python programming language. The statistical results and program are available from the online database: ion distribution in protein molecules (IDPM) at http://liulab.csrc.ac.cn/idpm/ . CONCLUSION:The spatial distribution of ions around amino acids is documented and analyzed. The statistics can be useful for identifying ion types for a given site in biomolecules, and can be potentially used in ion position prediction for given structures.

Dataset Information

AngioDB: database of angiogenesis and angiogenesis-related molecules.

Publications

AngioDB: database of angiogenesis and angiogenesis-related molecules.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets