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In last years relevant progress in the development and clinical use of drugs for treating HIV-1 infection has been made. The combined use of anti- AIDS drugs has significantly improved the clinical management of HIV-1 infection. Nevertheless, when antiretroviral therapy fails, new viral variants emerge, thus allowing HIV-1 to become resistant to drugs by accumulating mutations, either alone or in multiple patterns. Understanding the genetic basis of resistance and cross-resistance is essential for optimizing the use of existing drugs and for designing new antiviral agents. This book, therefore, provides new computational approaches aimed to rationalize the effects of known resistance- inducing mutations and to discover novel selective anti-HIV resistance-evading drugs. Three HIV-1 macromolecular targets crucial for viral fitness and replication have been analyzed: the reverse transcriptase, the protease and the envelope glycoprotein gp41. The medicinal chemist can use these approaches to predict the effects of certain HIV-1 PR relevant mutations in presence of novel inhibitors.