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 user's 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.