This issue isn't a matter for obedience training, it's an issue of behavior modification. Most aggressive behavior in dogs that I have observed as a professional trainer and behavior consultant are based in fear, as you suspect. One of the most effective methods for dealing with fear-related aggression is desensitization and counter-conditioning (D/CC) (1, 2). However, you should first take your dog to a good veterinarian for a thorough physical including blood workup. This is because some medical issues can manifest with aggressive actions as a symptom. If the vet gives a clean bill of health, then I recommend hiring a qualified dog behavior consultant or animal behaviorist (these are only vets who have a specialized training in animal behavior or graduates with a PhD in animal behavior). A good trainer with experience with dog aggression may be an appropriate alternative (ie, a qualified dog behavior consultant), just interview whomever you find to learn about both the quantity and QUALITY of their aggression experience and their education as well).
To get an idea of what the way D/CC works, see Barbara Brill's description of the process or that from the ASPCA. (3, 4). To find a nationally certified professional dog trainer in your area, go to the Certification Council for Professional Dog Trainers (http://tiny.cc/pqbkj) or check out trainers at International Association of Animal Behavior Professionals (http://tiny.cc/9u91m) or Association of Animal Behavior Professionals (http://tiny.cc/50jdu).
As a final note, for a fearful dog, creating more fear by using choke or prong collars, or worse punishers than those two, is NEVER a good idea and NEVER EVER a method of first resort. Fear plus pain typically creates worse fears. I strongly suggest ignoring any such advice.
BEST OF LUCK!
1) www.animalbehaviorassociates.com/book-pe... (Dr. Suzanne Hetts)
2) http://www.clickersolutions.com/interviews/bailey.htm (Bob Bailey)
3) http://aggressivebehaviorsindogs.com/content/view/35/44/ (Barbara Brill)
4) http://www.aspcabehavior.org/articles/14/Desensitization-and-Counterconditioning.aspx (ASPCA)
5) CCPDT (http://tiny.cc/pqbkj); IAABC (http://tiny.cc/9u91m); or AABP (http://tiny.cc/50jdu)