No internet connection except with browsers Win 7 Home Ed 64Bit?

This started happening after i downloaded something with a malware virus, the virus was downloading all these tool bars and programs i never accepted to downloading and changing my browsers home screen, ya know, the regular stuff, so i ran all my anti virus tools MalWareBytes, SuperAntiSpyware, and Microsoft security essentials. So that was done but then i realized certain programs i use were not connecting to the internet, i use MotioninJoy witch connects to a URL link to a page witch has all the stuff you need to configure my controller, and the Minecraft Launcher can only play Offline, oh and i can't update my anti virus tools like Security essentials witch is very bad, and also Windows Update don't work. So i really need this sorted out, i haven't got any past system Restore points so that not an option. But my browser (Google Chrome) works fine, but Internet Explorer won't connect to the internet. And my dads Laptop has no problems by the way, but anyway, thanks to any awnsers, hope i can fix this.