• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Journal of KIISE:Computing Practices and Letters
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• v.11 no.2
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• pp.133-148
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• 2005

Since understanding of similarities and differences among protein structures is very important for the study of the relationship between structure and function, many protein structure comparison systems have been developed. Hut, unfortunately, these systems introduce their own protein data derived from the PDB(Protein Data Bank), which are needed in their algorithms for comparing protein structures. In addition, according to the rapid increase in the size of PDB, these systems require much more computation to search for common substructures in their databases. In this paper, we introduce a protein structure comparison system named WS4E(A Web-Based Searching Substructures of Secondary Structure Elements) based on a PSAML database which stores PSAML documents using the eXist open XML DBMS. PSAML(Protein Structure Abstraction Markup Language) is an XML representation of protein data, describing a protein structure as the secondary structures of the protein and their relationships. Using the PSAML database, the WS4E provides web services searching for common substructures among proteins represented in PSAML. In addition, to reduce the number of candidate protein structures to be compared in the PSAML database, we used topology strings which contain the spatial information of secondary structures in a protein.

• The Journal of Korean Association of Computer Education
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• v.12 no.4
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• pp.57-64
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• 2009

Protein structure comparison is a task that requires a lot of computing resources because many atoms in proteins need to be processed. To address the issue, Grid computing environment has been employed for processing time-consuming jobs in a distributed manner. However, controling the Grid computing environment may not be easy for non-experts. In this paper, we present a JXTA-based system for protein structure comparison that can be easily controled by non-experts. To search proteins similar to a query protein, the geometric hashing algorithm that consists of preprocessing and recognition was employed. Experimental results indicate that the system can find the correct protein structure for a given query protein structure and the proposed system can be easily extended to solve the protein docking problem. It is expected that the proposed system can be useful for non-experts, especially users who do not have sophisticated knowledge of distributed systems in general such as college students who major in biology or chemistry.

• The KIPS Transactions:PartD
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• v.12D no.2 s.98
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• pp.247-258
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• 2005

Protein structure is highly related to its function and comparing protein structure is very important to identify structural motif, family and their function. In this paper, we construct an integrated database system which has all the protein structure data and their literature. The structure queries from the web interface are compared with the target structures in database, and the results are shown to the user for future analysis. To constructs this system, we analyze the Flat-File of Protein Data Bank. Then we select the necessary structure data and store as a new formatted data. The literature data related to these structures are stored in a relational database to query the my kinds of data easily In our structure comparison system, the structure of matched pattern and RMSD valure are calculated, then they are showed to the user with their relational documentation data. This system provides the more quick comparison and nice analyzing environment.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.10 no.6
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• pp.1399-1406
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• 2009

Proteins are one of essential part of organisms; many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Researching for 3D structure of proteins is important because functions of proteins are determined by 3D structure of them. In this study, we developed graphic tool that supports comparison and observation of the two proteins' 3D structure in the single screen. It also supports some comparison data to help researcher's easy comparison and observation works.

• Molecules and Cells
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• v.38 no.2
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• pp.105-111
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• 2015

The beta2-adrenergic receptor (${\beta}2AR$) belongs to the G protein coupled receptor (GPCR) family, which is the largest family of cell surface receptors in humans. Extra attention has been focused on the human GPCRs because they have been studied as important protein targets for pharmaceutical drug development. In fact, approximately 40% of marketed drugs directly work on GPCRs. GPCRs respond to various extracellular stimuli, such as sensory signals, neurotransmitters, chemokines, and hormones, to induce structural changes at the cytoplasmic surface, activating downstream signaling pathways, primarily through interactions with heterotrimeric G proteins or through G-protein independent pathways, such as arrestin. Most GPCRs, except for rhodhopsin, which contains covalently linked 11 cis-retinal, bind to diffusible ligands, having various conformational states between inactive and active structures. The first human GPCR structure was determined using an inverse agonist bound ${\beta}2AR$ in 2007 and since then, more than 20 distinct GPCR structures have been solved. However, most GPCR structures were solved as inactive forms, and an agonist bound fully active structure is still hard to obtain. In a structural point of view, ${\beta}2AR$ is relatively well studied since its fully active structure as a complex with G protein as well as several inactive structures are available. The structural comparison of inactive and active states gives an important clue in understanding the activation mechanism of ${\beta}2AR$. In this review, structural features of inactive and active states of ${\beta}2AR$, the interaction of ${\beta}2AR$ with heterotrimeric G protein, and the comparison with ${\beta}1AR$ will be discussed.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.131-140
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• 1998

The calcium-induced structural changes in the skeletal muscle regulatory protein troponin C (NTnC) involve a transition from a ‘closed’to an ‘open’structure with the concomitant exposure of a large hydrophobic interaction site for target proteins. Structural studies have served to define this conformational change and elucidate the mechanism of the linkage between calcium binding and the induced structural changes. There are now several structures of NTnC available from both NMR and X-ray crystallography. Comparison of the calcium bound structures reveals differences in the level of opening. We have considered the concept of a flexible open state of NTnC as a possible explanation for this apparent discrepancy. We also present simulations of the closed-to-open transition which are in agreement with the flexibility concept and with experimental energetics data.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.65-65
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• 2003

After many genome projects, algorithms and software to process explosively growing biological information have been developed. To process huge amount of biological information, high performance computing equipments are essential. If we use the remote resources such as computing power, storages etc., through a Grid to share the resources in the Internet environment, we will be able to obtain great efficiency to process data at a low cost. Here we present the performance improvement of the protein secondary structure prediction (PSIPred) by using the Grid platform, distributing protein sequence data on the Grid where each computer node analyzes its own part of protein sequence data to speed up the structure prediction. On the Grid, genome scale secondary structure prediction for Mycoplasma genitalium, Escherichia coli, Helicobacter pylori, Saccharomyces cerevisiae and Caenorhabditis slogans were performed and analyzed by a statistical way to show the protein structural deviation and comparison between the genomes. Experimental results show that the Grid is a viable platform to speed up the protein structure prediction and from the predicted structures.

• The KIPS Transactions:PartB
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• v.16B no.5
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• pp.359-366
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• 2009

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure alignment is the main subjects of the structural bioinformatics and the most fundamental problem. Protein Structures are flexible and undergo structural changes as part of their function, and most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. We present a new method that carries out the flexible structure alignment by means of finding SSPs(Similar Substructure Pairs) and flexible points of the protein. In order to find SSPs, we encode the coordinates of atoms in the backbone of protein into RDA(Relative Direction Angle) using local similarity of protein structure. We connect the SSPs with Floyd-Warshall algorithm and make compatible SSPs. We compare the two compatible SSPs and find optimal flexible point in the protein. On our well defined performance experiment, 68 benchmark data set is used and our method is better than three widely used methods (DALI, CE, FATCAT) in terms of alignment accuracy.

• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.