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分子影像工具與來源Molecular Graphics Tools and Resources
| RCSB蛋白質資料庫The RCSB Protein Data Bank |
蛋白質資料庫是單一的世界性儲藏庫: 提供處理與散佈3-D生物性巨分子結構資料。The Protein Data Bank is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. |
PDB |
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 〈蛋白質資料庫〉《核甘酸研究》 28 (2002): 235-242.Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. "The Protein Data Bank." Nucleic Acids Research 28 (2002): 235-242. |
| Deep View Swiss PDB Viewer |
The Deep View Swiss-Pdb Viewer提供使用者友善的介面以利同時分析多種蛋白質。The Deep View Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. |
Deep Viewer |
Guex, N., and M. C. Peitsch. 〈SWISS-MODEL 與 Swiss-Pdb Viewer: 利於比較蛋白質模組的環境〉 《電泳》 18 (1997): 2714-2723. Guex, N., and M. C. Peitsch. "SWISS-MODEL and the Swiss-Pdb Viewer: An Environment for Comparative Protein Modeling." Electrophoresis 18 (1997): 2714-2723. |
| 生物技術資訊國家中心National Center for Biotechnology Information |
成立於1988，為一分子生物資訊的國家型資源。NCBI創造了公共的資料庫，以計算化生物系統進行研究，發展出分析基因組資料的軟體工具，以及傳播生物醫學資訊- 這都有助於我們更了解影響人類健康與疾病的分子過程。Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
這個網站提供了無數的序列資料庫，結構資料庫，生物資訊工具，以及文獻搜尋工具。This Web site provides access to a myriad of biological sequence databases, structural databases, bioinformatics tools, and literature search tools.
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| 基本的個別電腦上比對搜尋工具(BLAST)Basic Local Alignment Search Tool |
BLAST提供一個快速搜尋核甘酸與蛋白質資料庫的方法。它是一個最佳化的序列比對演算法:為了能讓在搜尋序列資料庫的速度加快，而做了個別電腦上比對要求的最佳化。BLAST provides a method for rapid searching of nucleotide and protein databases. It is a sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. |
BLAST |
Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 〈基本的個別電腦上比對搜尋工具〉 《J. Mol》 Biol. 215 (1990): 403-410.Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. "Basic Local Alignment Search Tool." J. Mol. Biol. 215 (1990): 403-410.
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| ClustalW 排列比對ClustalW Alignment |
ClustalW是適用於DNA或蛋白質的一般性目的多序列排列比對。在不同的序列上，它可產生有生物意義的多序列比對。ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. |
ClustalW Alignment |
Higgins, D., J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins, and T. J. Gibson. 〈CLUSTAL W: 藉由序列測重、專一性位置缺口損失、以及測重母體選擇，來改善先進多序列比對的敏感度。〉 《Nucleic Acids Res》 22 (1994): 4673-4680.Higgins, D., J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins, and T. J. Gibson. "CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice." Nucleic Acids Res. 22 (1994): 4673-4680.
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| RASMOL |
RasMol為一分子成像軟體，可用在蛋白質、核甘酸與小分子的視覺化。這個軟體讀取分子協同檔案並以互動、多種呈現方式與色彩，顯示於畫面上。 支援輸入的檔案格式包括了Brookhaven蛋白質資料庫(PDB), Tripos Associates' Alchemy and Sybyl Mol2 格式, Molecular Design Limited's (MDL) Mol 檔案格式, Minnesota Supercomputer Centre's (MSC) XYZ (XMol)格式，以及CHARMm格式檔案. 不同的分子部位也許會以異於其他部位的顏色或是同時多種顯示來表達。RasMol可以從'script'檔案(有 *.spt副檔名)來讀取準備指令列表，用以讓已知的影像或是視點可以快速再產生。RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program reads in molecular co-ordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Brookhaven Protein Databank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Centre's (MSC) XYZ (XMol) format and CHARMm format files. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. RasMol can read a prepared list of commands from a 'script' file (with a *.spt extension) to allow a given image or viewpoint to be regenerated quickly. |
RASMOL |
Sayle, Roger, 與 E. James Milner-White. 〈RasMol: 生物分子影像大全〉 《生物化學科學趨勢》(TIBS) 20, no. 9 (九月 1995): 374.Sayle, Roger, and E. James Milner-White. "RasMol: Biomolecular Graphics for all." Trends in Biochemical Sciences (TIBS) 20, no. 9 (September 1995): 374.
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