All belief systems (theism, atheism, agnosticism, polytheism, etc.) are all held without full proof, and as such fall under the the study of philosophy. Science and philosophy are completely different subjects. Science cannot deny or justify atheism, and it cannot deny or justify theism. Science can only refute based upon logic and facts. If you take philosophy in college, it is usually in a completely different building than the science courses.
Atheism is not a belief system. Atheism is a position in response to a single claim. God exists. If you do not believe God exists you are an atheist, if you believe there is insufficient evidence to believe in God, you are an atheist. In other terms a belief system is presented and atheists reject the presented belief system as lacking sufficient evidence to be supportable.