The opposite of exploring 'natural responses' to attack is when you respond in a contrived manner. You deliberately limit yourself to a certain drill or movement and practice that.
Your partner attacks with a variety of strikes and grapples, whilst you carefully think your way through each response. Be slow and thoughtful; contemplate what you are doing and why. Do not rush this. Do not lose your whole-body response at any point.
Be aware of where you are leading your opponent and what the effect of each counter-strike will be.
This type of work helps you to practice form applications and drills against a wider range of attacks, and the results should feed into the natural responses training.
Remember that scientific analysis, form applications and partner drills are all contrived. Natural responses training is what you will use in self defence: it is the proof of where you are. What comes out, comes out.
If you are faced with a legitimate threat and take time to think, you will fail. The tendency to do this can be removed through melee training, in which the thinking time is removed by the immediacy and variety of the threat.