Yes, you can configure WebsitePanel to assign a dedicated application pool to each website while creating it. Please refer to below article for step by step guidance:
https://manage.accuwebhosting.com/knowledgebase/2054/Configure-WebsitePanel-to-automatically-assign-dedicated-application-pool-when-website-is-being-created.html
If you do not have WebsitePanel, you can assign a dedicated application pool while adding a new website from IIS. While adding a website from IIS, you will get an option to create a separate application pool for your website.
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