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Are you So whatever your DVD backup needs, give it a try. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings.

HIV reverse transcriptase is a a well-studies protein that is targeted by several existing anti-AIDS drugs such as nevirapine and efavirenz , and etravirine. One of the serious issues with HIV treatment is the emergence of drug resistance due to mutations; indeed mutations resistant to existing non-nucleoside HIV reverse transcriptase inhibitors are known. It would thus be interesting to develop analogs that can effectively inhibit these mutant forms of HIV reverse transcriptase.

Docking of the ligand that was originally present in the crystal structure to the same protein is one of the easiest docking tasks. Many docking programs correctly identify a ligand pose very similar to the experimentally observed pose as one with one with the highest score. The success of such re-docking does not always indicate that the docking of novel compounds will be reliable with the same program.

First, comparison of novel compounds involves scoring of these compounds against each other; this step is not needed for docking a single compound. Second, the shape of the binding pocket during docking of novel compounds is usually not allowed to change to accommodate the novel ligand, and thus ligands larger than the original ligand may not fit into the pocket according to the docking program.

In reality, proteins are flexible, and it is likely that the active site will change slightly to accommodate slightly larger ligands that otherwise make good contacts with the receptor. You can prove this by trying to dock known HIV reverse transcriptase inhibitors.