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Introduction
The NCTU Bioinformatics and Systems Biology Institute is the first Institute of Bioinformatics and is ranked among the best in Taiwan, as evidenced by the excellence of the faculty and students as well as the quality of interdisciplinary educational programs. The Major is designed for highly motivated students interested in interdisciplinary activities in life sciences, computer science, statistics, systems biology, and computational biology. Leading the Institute's research and teaching activities are 10 professors and 5 core facilities (e.g. over 300-cpu PC clusters and 40 MAC computers). The Institute has over 28 and 40 graduate students pursuing master and doctorate degrees, respectively.
The NCTU Institute of Bioinformatics and Systems Biology carries out research in structural bioinformatics, systems biology (e.g. gene networks and metabolic pathways), drug discovery, biological databases and algorithms, molecular evolution, computational chemistry, and functional genomics. Supporting by National Science Council and Ministry of Education, the Institute has installed the sole Structural Bioinformatics and Computer-aided Drug Design Core Facilities. On average, each faculty publishes 5 papers/year and the sum of impact factor is over 20/year; and the grant is over 3,000,000/year. These Principle Investigators have produced renowned computational packages and databases: GEMDOCK, for drug design; 3D-BLAST, for a super fast structure database search; miRNAMap, genomic maps of microRNAs in mammalian genomes; and CELLO, for sub-cellular localization prediction.
Research Highlights
 | [ Jen-Shiang Yu ] ANGEWANDTE CHEMIE-INTERNATIONAL EDITION - 2008
Remarkably short metal-metal bonds: A lantern-type quintuply bonded Dichromium(I) complex
The field of quadruply bonded dinuclear complexes in which two metal atoms are embraced by eight ligands has been considered mature. The bonding and electronic structures of these compounds have been well understood, ever since the discovery of the first dimetal species containing a quadruple bond, [Re2Cl8]2-, over 40 years ago. The quest for thermally stable and isolable dinuclear complexes with higher bond orders is one aim of chemists in this field.... Read more |
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 | [ Yeong-Shin Lin ] PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS - Oct. 2008
Using a strategy based on the concept of convergent evolution to identify residue substitutions responsible for thermal adaptation
Factors that are related to thermostability of proteins have been extensively studied in recent years, especially by comparing thermophiles and mesophiles. However, most of them are global characters. It is still not clear how to identify specific residues or fragments which may be more relevant to protein thermostability. Moreover, some of the differences among the thermophiles and mesophiles may be due to phylogenetic differences instead of thermal adaptation.... Read more |
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 | [ Jinn-Moon Yang ] PROTEIN ENGINEERING DESIGN & SELECTION - Sep. 2008
Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase
To obtain an enzyme for the production of chito-disaccharides (GlcN(2)) by converting endo-chitosanase to exo-chitosanase, we chose an endo-chitosanase from Bacillus circulans MH-K1 (Csn) as the candidate for protein engineering. Using molecular modeling, two peptides with five amino acids (PCLGG) and six amino acids (SRTCKP) were designed and inserted after the positions of D(115) and T(222) of Csn, respectively.... Read more |
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 | [ Jinn-Moon Yang ] Bioinformatics - Aug. 2008
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database
MOTIVATION: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35% of these have known substrates, while 14% of the kinases have identified substrate recognition motifs. In contrast, 85% of the kinases have protein-protein interaction (PPI) datasets, raising the possibility that we might reveal potential kinase-substrate pairs from these PPIs.... Read more |
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 | [ Chin Lung Lu ] NUCLEIC ACIDS RESEARCH - Jul. 2008
SARSA: a web tool for structural alignment of RNA using a structural alphabet
SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities.... Read more |
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 | [ Hsien-Da Huang ] NUCLEIC ACIDS RESEARCH - Jul. 2008
RNALogo: a new approach to display structural RNA alignment
Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation.... Read more |
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Highly Accessed Resources
 | Hwang JK Proteins. 2006 Aug 15;64(3):643-51.
Prediction of protein subcellular localization.
Because the protein's function is usually related to its subcellular localization, the ability to predict subcellular localization directly from protein sequences will be useful for inferring protein functions. Recent years have seen a surging interest in the development of novel computational tools to predict subcellular localization.... Read more |
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 | Yang JM Nucleic Acids Res. 2007 Jul;35(Web Server issue):W438-43. Epub 2007 May 7.
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.
The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with <95% identity with each other) and the top 10 hit domains, which have different superfamily classifications, are obtained from the hit list.... Read more |
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 | Huang HD Nucleic Acids Res. 2008 Jan;36(Database issue):D165-9. Epub 2007 Nov 19.
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
MicroRNAs (miRNAs) are small non-coding RNA molecules that can negatively regulate gene expression and thus control numerous cellular mechanisms. This work develops a resource, miRNAMap 2.0, for collecting experimentally verified microRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes. Three computational tools, miRanda, RNAhybrid and TargetScan, were employed to identify miRNA targets in 3'-UTR of genes as well as the known miRNA targets.... Read more |
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