StrandPairsViewer: a toolkit for visualization and analysis of amino acids pairs in protein sheet structures
Amino acids (AAs) pairs in protein sheets structures have turned out to be important in studying protein tertiary structures and protein folding pathways.Most existing software tools are sophisticated in visualizing and manipulating protein 3-D structures.However, these tools are inconvenient to retrieve strands alignment information and are not so intuitive to illustrate the AAs pairs on strands.In the present study, we present a new software toolkit, called StrandPairsViewer, which can read protein structures data in PDB file and extract AAs pairs as well as peptide chain sequences, sheet structures and strand alignments.It can demonstrate AAs pairs in an intuitive color text that can be pasted into other word-processing software for further editing.The toolkit also supports aligning coding nucleic acid sequences along with the paired strands in color for finding additional folding information from nucleic acids.StrandPairsViewer also enables to make statistical analysis on AAs pairs, as well as manage users dataset effectively.The proposed toolkit has a convenient and intuitive interface that is potentially helpful and may assist in the protein structures and protein folding study, as a useful complement to the existing visualization tools for protein 3-D structures.The proposed toolkit with a User Manual and sample data files can be accessed on the internet at http://sky.nankai.edu.cn/script/sky/english/bioinformatics/psv.zip
protein structure sheet amino acids pair visualization
Ning ZHANG Shan GAO Guang-You DUAN Zhuo YANG Tao ZHANG
Key Lab.of Bioactive Materials,Ministry of Education and the College of Life Sciences Nankai Univers College of Medicine Science Nankai University Tianjin,PR China,300071
国际会议
北京
英文
1-4
2009-06-11（万方平台首次上网日期，不代表论文的发表时间）