The scientist explained that water turns to steam when heated to 100 degrees.
in place of 'classically' standard (if marginally less natural-sounding)
[1a] The scientist explained that water turned to steam when heated to 100 degrees.
, the same is not true of structurally analogous
 *I thought you are my friend.
, which cannot be substituted for
[2a] I thought you were my friend.
and note that its unacceptability is quite unrelated to the presence or otherwise of any intended implication as to the current state of my beliefs, our friendship, or anything else.
In view of this complex case-sensitive 'continuum' of acceptability, running the gamut from  (completely acceptable, except perhaps for the most formal academic writing) to  (completely unacceptable) - with any number of indeterminate cases falling between these two extremes upon which even natives might disagree! - the learner would clearly be better advised to follow what is, after all, a very clear and eminently learnable transformation rule than to risk producing a non-sentence.