1.Protein Backbone Torsion Angle-Based Structure Comparison and Secondary Structure Database Web Server.
Sunghoon JUNG ; Se Eun BAE ; Insung AHN ; Hyeon S SON
Genomics & Informatics 2013;11(3):155-160
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.
Databases, Protein
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Protein Structure, Secondary
3.WinBioDBs: A Windows-based Integrated Program for Manipulating Major Biological Databases.
Hyeweon NAM ; Jin Ho LEE ; Kiejung PARK
Genomics & Informatics 2009;7(3):175-177
We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.
Abstracting and Indexing as Topic
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Databases, Nucleic Acid
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Databases, Protein
4.Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability.
Yoo Jin CHUN ; Seong Il HAM ; San Duk YANG ; Arang RHIE ; Hyun Seok PARK
Genomics & Informatics 2008;6(1):50-53
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Computational Biology
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Databases, Protein
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Indonesia
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Proteins
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Software
5.Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability.
Yoo Jin CHUN ; Seong Il HAM ; San Duk YANG ; Arang RHIE ; Hyun Seok PARK
Genomics & Informatics 2008;6(1):50-53
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Computational Biology
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Databases, Protein
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Indonesia
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Proteins
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Software
6.SFannotation: A Simple and Fast Protein Function Annotation System.
Genomics & Informatics 2014;12(2):76-78
Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these databases often causes a bottleneck for rapid functional annotation. We developed SFannotation, a simple and fast functional annotation system that rapidly annotates putative proteins against four extant databases, Swiss-Prot, TIGRFAMs, Pfam, and the non-redundant sequence database, by using a best-hit approach with BLASTP and HMMSEARCH.
Computational Biology
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Databases, Protein
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Molecular Sequence Annotation
7.Proteomics and peptidomics analysis of Sepiae Endoconcha.
Rui LIU ; Shuang WEI ; Xin-Zhi WANG ; Jian-Ming CHENG ; Hao WU
China Journal of Chinese Materia Medica 2020;45(16):3883-3889
Shotgun based proteomics and peptidomics analysis were used to investigate the proteins and peptides in marine traditional Chinese medicine(TCM) Sepiae Endoconcha(cuttlebone). Peptides were extracted from cuttlebone by acidified methanol, and then strong cation exchange(SCX) resin was used to enrich those peptides. Also, proteins from cuttlebone were extracted and digested by trypsin. nano-LC Q Exactive Orbitrap mass spectrometry was used to analyze proteins and peptides from cuttlebone. As a result, a total of 16 proteins and 168 peptides were identified by protein database search, and 328 peptides were identified by De novo sequencing. The identified proteins were hemocyanin, enolase, myosin, actin, calmodulin, etc., and the identified peptides were derived from actin, histone, and tubulin. All these proteins and peptides were important components in cuttlebone, which would provide important theoretical and research basis for marine TCM cuttlebone investigations.
Cations
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Databases, Protein
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Mass Spectrometry
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Peptides
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Proteomics
8.Quaternion-based Characterization of Protein α Helix.
Journal of Biomedical Engineering 2016;33(1):155-160
This paper proposes a method based on quaternion for characterization a helix of proteins. The method defines the parameter called Quaternion Helix Axis Spherical Distance (QHASD) on the basis of mapping protein Cα frames' helical axis onto a unit sphere, and uses QHASD to characterize the a helix of the protein secondary structure. Application of this method has been verified based on the PDBselect database, with an a helix characterization accuracy of 91.7%. This method possesses significant advantages of high detection accuracy, low computation and clear geometric significance.
Algorithms
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Databases, Protein
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Models, Molecular
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Protein Structure, Secondary
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Proteins
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chemistry
9.Construction of nervous system relative protein and gene secondary database.
Pan WANG ; Xinhao CHEN ; Xiangming LIU
Journal of Biomedical Engineering 2007;24(5):1023-1026
Along with the rapid research of neural molecular biology, abundant data are produced so that the collection and coordination of high-throughout data about nervous system relative proteins and genes are imperative. Through analyzing the biological primary databases maintained by NCBI and RCSB as the main data source and designing a new data model, a local specialized secondary database is constructed, which mainly includes nucleotide sequences, protein sequences and protein structures, and is established on Sun Blade 2000 System and Oracle 9i. All programs are developed by Java technology. A method of web information automatic retrieval with XML is proposed for sequence data collection and submission to the database. JSP + JavaBean technology is used to support data promulgation on Internet. The establishment of this database provides an excellent platform for the research of neural molecular biology and the pathogenesis of related diseases.
Database Management Systems
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Databases, Nucleic Acid
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Databases, Protein
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Gene Expression Profiling
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Humans
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Nervous System
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Proteins
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chemistry
10.A Pattern Summary System Using BLAST for Sequence Analysis.
Han Suk CHOI ; Dong Wook KIM ; Tae W RYU
Genomics & Informatics 2006;4(4):173-181
Pattern finding is one of the important tasks in a protein or DNA sequence analysis. Alignment is the widely used technique for finding patterns in sequence analysis. BLAST (Basic Local Alignment Search Tool) is one of the most popularly used tools in bio-informatics to explore available DNA or protein sequence databases. BLAST may generate a huge output for a large sequence data that contains various sequence patterns. However, BLAST does not provide a tool to summarize and analyze the patterns or matched alignments in the BLAST output file. BLAST lacks of general and robust parsing tools to extract the essential information out from its output. This paper presents a pattern summary system which is a powerful and comprehensive tool for discovering pattern structures in huge amount of sequence data in the BLAST. The pattern summary system can identify clusters of patterns, extract the cluster pattern sequences from the subject database of BLAST, and display the clusters graphically to show the distribution of clusters in the subject database.
Computational Biology
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Databases, Protein
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DNA
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Sequence Analysis*
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Sequence Analysis, DNA