In present work, we have performed molecular docking and 3D QSAR analysis of quinoxaline derivatives, previously reported as potential influenza NS1A protein inhibitors..The docking analysis reveals that presence of water molecule inside the cavity of receptor play very crucial role. For better outcome, receptor based electrostatic potential map are also analyzed. The QSAR model is robust, statistically sound and validated thoroughly to avoid over fitting and chancy correlations. The three parametric model is with R2 = 0.874, adj. R2 = 0.859, pred. R2 = 0.805, F value = 60.196. The analysis indicates that the biologic activity depends upon 3D descriptors. Combined use of different types of 3-D descriptors like WHIM, GATEAWAY and 3D MoRSE afforded valuable QSAR model. The analysis could be very useful in designing better influenza NS1A protein inhibitors.
