PARM: a practical utility for drug design.

To accommodate situations in which the 3D structure of the target receptor is not available, we have developed the Pseudo Atomic Receptor Model (PARM) software package. In this article we describe PARM and illustrate its use with three examples: elemenes (potential anticancer drugs), angiotensin converting enzyme inhibitors, and human HIV-1 inhibitors TTD (1,1,3-trioxo-2H, 4H-thieno[3,4-e][1,2,4] thiadiazine derivatives). The results show that PARM can build models with favorable cross-validation statistics (Rcv2 values 0.7-0.9) and give helpful SAR insight. PARM has certain advantages: (a) it can be used for many systems, regardless of whether the 3D structure of the receptor is known; (b) PARM models were demonstrated to be highly statistically reliable; and (c) PARM analyses are robust and reproducible.