A structure-based molecular modeling approach was performed to identify novel structural characteristics and scaffolds that might represent new classes of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). The software LigandScout was used for identification and visualization of protein-ligand interaction sites and pharmacophore model generation. In the next step virtual screening of 3D multiconformational databases together with docking experiments allowed the identification of promising candidates for biological testing. The positive biological results obtained confirm the validity of our work strategy.