It all depends on what kind of eBook you're thinking of.
A PDF itself is really a kind of eBook, but it has no rights management, modest (potential) security, limited interactive features, and uses page-layout presentation (that is, the layout is fixed, and the pages look exactly as you designed them).
Then there's a variation on PDF that's got rights management via Adobe Digital Editions, but this platform hasn't evolved much in recent months.
An ePUB file (exported from InDesign) is designed to be tweaked to make it work with various eReaders (Kindle, iBooks, Nook, etc.), but these schemes don't preserve the layout. Instead they "reflow" the text when the user changes the display width or height, or the font size or line spacing. Currently, these readers tend not to support much in the way of fonts and formatting, and have limited multi-media capabilities (if any).
Then there's the uber-geek total control approach -- a stand-alone Flash file with whatever elaborate interaction you like, from soup to nuts, along with total control over layout and presentation. This kind of document could have any sort of rights management and features you want, but it would probably be completely hand made, and would likely require serious programming experience.
And finally there's what I call eMags -- elaborate, colorful, interactive publications based on the newest tools for presenting periodicals on tablet computers and others. This is where the Adobe Digital Publishing Suite comes in. Using document design tools in InDesign, and support from commercial services provided by Adobe (for a significant fee), you can create and publish magazines like Wired and The New Yorker and many others.
If you're just looking to make something available as a downloadable book, and you're not worried about large-scale rip-offs, and you want total control over the design, and you don't need much interactivity, PDF is probably the best way to get started.
If you're aiming for the Kindle, you'll be publishing (distributing and selling) through Amazon, and you would start with InDesign's export to ePUB format, and then learn (with the rest of us) the best way to optimize your book for Kindle viewing. But you wouldn't be selling the Kindle version on your site -- you'd link to the Kindle edition on Amazon.
I hope this helps.
Thank you for your answer!
I would like to create a version like this:
I have a lot of PDF files which I would like to upload on my website for my students in this form...
The students could get their information regarding these e-papers...
Is this possible to create with InDesign 5.5?
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These eBooks are essentially PDF pages wrapped in a Flash program that acts as a custom reader and adds protection, shading, page flipping animation, etc.
You can get part way to this with PDF by itself (in full screen mode there is a fairly attractive page-flip effect), but InDesign can't produce the Flash wrapper that contains the PDF.
It sounds like your first step is to build the PDF. Explore the Adobe Reader and the PDF features available in InDesign. If the PDF by itself isn't all that you need, then you can convert it to a Flash-based reader with one of these services.