The unfortunate answer is, there isn't a good way to do it. No journal would accept a paper on just the scoring application by itself, and generally none would accept something just documenting the existing scorefunction either. We as a community are frustrated by the lack of a citation for what you want, too.
Immediately, your best bets to cite either the Rohl methods in enyzmology paper (PMID: 15063647) which discusses most of the scorefunction terms, or the Kuhlman paper on top7 which discusses them in the supplemental (PMID:14631033). There is a paper coming (O'Meara et al) which will describe the scorefunction balance in detail (along with a method for scorefunction optimization, which is what makes it interesting and novel for publication) and will serve wonderfully for this purpose...but it's not out yet.
The unfortunate answer is, there isn't a good way to do it. No journal would accept a paper on just the scoring application by itself, and generally none would accept something just documenting the existing scorefunction either. We as a community are frustrated by the lack of a citation for what you want, too.
Immediately, your best bets to cite either the Rohl methods in enyzmology paper (PMID: 15063647) which discusses most of the scorefunction terms, or the Kuhlman paper on top7 which discusses them in the supplemental (PMID:14631033). There is a paper coming (O'Meara et al) which will describe the scorefunction balance in detail (along with a method for scorefunction optimization, which is what makes it interesting and novel for publication) and will serve wonderfully for this purpose...but it's not out yet.