Quantitative Structure-Activity Relationship (QSAR) studies were performed on a series of N-acyl amino acids and imidazopyrazines/pyridines derivatives with the help of PM5 calculations and geometry optimizations using Cache software. Multiple Linear Regression (MLR) analysis was performed to derive QSAR models using the descriptors, molecular weight (MW), conformation minimum energy (), HOMO energy (HOMO), solvent accessibility surface area (SASA), molar volume (MV), molar refractivity (MR), LogP (LP) and parachor (Pc). The QSAR model equations of anti-ulcer agents have been developed by using maximum of seven descriptors, in which conformation minimum energy, molar volume and parchor were present have an excellent predictive powers of correlation and cross validation coefficients. These models can successfully predict the anti-ulcer activity of any newly discovered N-acyl amino acids and imidazopyrazines/pyridines derivatives which can later be tested in laboratory.