Hi Cuixia, I am old fashion. In silico, everything might work out great on a computer screen, but you will never know how peptides affect cells until you try them.

The "wet work" required of examining how peptides interact with cells is a quantum leap from what they do in computer models.    

You can initially do in silico studies on peptides to identify already reported bioactivity using   Peptide ranker and BIOPEP database and then perform molecular docking for followed by in vitro validation assays for the lead peptides.

Many thanks to Viji Viji ,Steingrimur Stefansson,Petar Žuvela, and Aparna H S. Thanks for your constructive advice.  I have some peptides. The function is unknow in the cell. According your advice. Firstly, I should do  silico studies to find its target in the cell. Secondly, I need to examine how peptides interact with cells, using invitro validation.

A good way to go about would be subject the peptides to interaction analysis such as by using STRING or DAVID. You would be able to see that how homologous sequences interact with the cell, including the most likely pathways and molecules that would be involved. Then, you may further study each type of interaction in detail by docking and simulation studies.