Biomedical subjects

Insoo Jang

Publications and source records attributed to Insoo Jang.

4 recordsLinked to original sources

PubMed2006

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information.

The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein domain database called LocaloDom. LocaloDom is a curated database that contains TM topologies and TM helix numbers of known protein domains. It was constructed from Pfam domains combined with Swiss-Prot annotations and Phobius predictions. The Localizome server corrects the combined results of the user sequence to conform to the rules stored in LocaloDom. Compared with other programs, this server showed the highest accuracy for TM topology prediction: for soluble proteins, the accuracy and coverage were 99 and 75%, respectively, while for TM protein domain regions, they were 96 and 68%, respectively. With a graphical representation of TM topology and TM helix positions with the domain units, the Localizome server is a highly accurate and comprehensive information source for subcellular localization for soluble proteins as well as membrane proteins. The Localizome server can be found at http://localizome.org/.

Cell Compartmentation↗

PubMed2005

A protein domain interaction interface database: InterPare.

BACKGROUND: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently. DESCRIPTION: We introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net. It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website. CONCLUSION: InterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance), 10,431 (ASA), and 11,010 (Voronoi diagram) entries in the Protein Data Bank (PDB) containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain-domain interaction interfaces and 12,758 intra-chain domain-domain interfaces.

Computers, Molecular↗

PubMed2005

PSIbase: a database of Protein Structural Interactome map (PSIMAP).

UNLABELLED: Protein Structural Interactome map (PSIMAP) is a global interaction map that describes domain-domain and protein-protein interaction information for known Protein Data Bank structures. It calculates the Euclidean distance to determine interactions between possible pairs of structural domains in proteins. PSIbase is a database and file server for protein structural interaction information calculated by the PSIMAP algorithm. PSIbase also provides an easy-to-use protein domain assignment module, interaction navigation and visual tools. Users can retrieve possible interaction partners of their proteins of interests if a significant homology assignment is made with their query sequences. AVAILABILITY: http://psimap.org and http://psibase.kaist.ac.kr/

Binding Sites↗

PubMed2003

A study on the central neural pathway of the heart, Nei-Kuan (EH-6) and Shen-Men (He-7) with neural tracer in rats.

The purpose of this morphological study was to investigate the relations between meridians, acupoints and viscera using neuroanatomical tracers. The labeled areas of the spinal ganglia, sympathetic chain ganglia, spinal cord and the brain projecting to the heart, Nei-Kuan (EH-6) and Shen-Men (He-7) were observed following injection of WGA-HRP and pseudorabies virus (PRV). The results were as follows. Overlapping bilaterally labeled ganglion areas after heart, Nei-Kuan (EH-6) or Shen-Men (He-7) injection of WGA-HRP were found in middle cervical, stellate and T4 sympathetic and T2-T6 spinal ganglia. In brain, labeled neurons from all three sites were found in the A1 noradrenalin cell group/C1 adrenalin cell group/caudoventrolateral reticular n., n. tractus solitarius, n. ambiguus, rostroventrolateral n., C3 adrenaline cell group, raphe obscurus n., raphe pallidus n., raphe magnus n., lateral paragigantocellular reticular n., locus coeruleus, subcoeruleus n., Kolliker-Fuse n., A5 cell group, central gray matter, paraventricular hypothalamic n. and arcuate hypothalamic n.. In conclusion, these morphological results suggest that the interrelationship of acupoints (Nei-Kuan and Shen-Men) and viscera (heart) may be related to the central autonomic centers of the spinal cord and brain.

Acupuncture Points↗