I'm going to make some assumptions here - that you've observed the aggressive cat preventing the other cat from approaching the litter box or otherwise bullying the more timid cat, and that the two cats aren't getting on terribly well.
In this situation, your best bet is to make a closable room a refuge for the timid cat (similar to what's recommended to stop middening). The room will need a selection of cat toys for your timid cat, a lot of things that smell of you, and a litter box, food, and water.
You'll need to spend plenty of time in the room with the timid cat (if you have a study with a closable door, this is perfect). You'll also want to provide a place in the room where the timid cat can hide and feel safe. The recommendations for middening are that it will usually take a week or so for the cat to relax. You will want to change the items in the room around a bit (you want to make sure the timid cat is relaxed even with items that smell of the aggressive cat).
In time both cats should start getting lonely and trying to play with each other by poking paws under the door. At this point, you can bring the timid cat out for some supervised time in the aggressive cat's company. If the aggressive one starts bullying, take the timid one back to the sanctuary, and leave both alone for a while (you don't want the timid cat associating being bullied with getting your attention any more than you want the aggressive one associating bullying with getting your attention). Rinse and repeat until both cats are relatively calm in each others presence.
If this method fails, then the last ditch is to get one of those expensive cat doors with a key and put the cat door in the door to the timid cat's sanctuary. The timid cat gets to wear the collar with the key so it has somewhere to go that the aggressive cat can't reach it. As long as the timid cat has litter, food, water, and toys in there, you shouldn't have any more messes.