BackgroundThe AutoDock family of software has been widely used in protein-ligand docking research. This study compares AutoDock 4 and AutoDock Vina in the context of virtual screening by using these programs to select compounds active against HIV protease.Methodology/Principal FindingsBoth programs were used to rank the members of two chemical libraries, each containing experimentally verified binders to HIV protease. In the case of the NCI Diversity Set II, both AutoDock 4 and Vina were able to select active compounds significantly better than random (AUC = 0.69 and 0.68, respectively; p<0.001). The binding energy predictions were highly correlated in this case, with r = 0.63 and ι = 0.82. For a set of larger, more flexible compounds from the Directory of Universal Decoys, the binding energy predictions were not correlated, and only Vina was able to rank compounds significantly better than random.Conclusions/SignificanceIn ranking smaller molecules with few rotatable bonds, AutoDock 4 and Vina were equally capable, though both exhibited a size-related bias in scoring. However, as Vina executes more quickly and is able to more accurately rank larger molecules, researchers should look to it first when undertaking a virtual screen.

Effective strategies are needed to block mucosal transmission of human immunodeficiency virus type 1 (HIV-1). Here, we address a crucial question in HIV-1 pathogenesis: whether infected donor mononuclear cells or cell-free virus plays the more important role in initiating mucosal infection by HIV-1. This distinction is critical, as effective strategies for blocking cell-free and cell-associated virus transmission may be different. We describe a novel ex vivo model system that utilizes sealed human colonic mucosa explants and demonstrate in both the ex vivo model and in vivo using the rectal challenge model in rhesus monkeys that HIV-1-infected lymphocytes can transmit infection across the mucosa more efficiently than cell-free virus. These findings may have significant implications for our understanding of the pathogenesis of mucosal transmission of HIV-1 and for the development of strategies to prevent HIV-1 transmission. N ovel microbicide and vaccine candidates for human immunodeficiency virus type 1 (HIV-1) are being evaluated preclinically for efficacy by assessing their ability to protect nonhuman primates against cell-free simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV) challenges. However, it remains unclear whether cell-associated virus (virus-infected donor mononuclear cells), cell-free virus, or both play the most important roles in initiating mucosal infection by HIV-1 (1-5). This distinction is critical, since effective strategies for blocking cell-free and cell-associated virus transmission may be very different (3, 6, 7). We sought to explore early events in mucosal transmission of HIV-1 and SIV by evaluating the relative efficiency of cell-associated and cell-free virus in initiating mucosal infection. To model these infection events, we developed a novel three-dimensional sealed human colonic mucosa explant system. We utilized this system in association with the SIV distal colon in vivo challenge model in rhesus macaques to evaluate the relative efficiency of initiating mucosal infection using cell-associated virus compared to that of initiating mucosal infection using cell-free virus in vivo. MATERIALS AND METHODS Viruses.A replication-competent CC chemokine receptor type 5 (CCR5)-tropic HIV-1 strain expressing green fluorescence protein (GFP) [HIV-1(R5) NL4.3-BaL-GFP] (8) was utilized for human organ infections, and SIVmac251 (9) was utilized for rhesus monkey tissue infections.TCID 50 for cell-associated virus and cell-free virus. The 50% tissue culture infective dose (TCID 50 ) was determined as previously described (10). Briefly, 4 replicates each of cell-associated virus (starting with 200,000 cells/well) and cell-free virus (starting with concentrated virus) were added to the first column of a 96-well plate. Then, 5-fold dilutions were performed for a total of 9 serial dilutions (1:5 to 1:5 9 ). An additional column with no virus or cells added served as a negative control to measure the background. TZM-bl cells (NIH AIDS Research and Reference Reagent Pr...