Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN.

Lutein: a new dye for chromovitrectomy.

Purpose: To evaluate the feasibility, advantages, and safety of a novel lutein-based dye for improving identification and removal of the vitreous, internal limiting membrane, and epiretinal membrane during chromovitrectomy in humans.

Methods: We prospectively evaluated 12 eyes that underwent pars plana vitrectomy using the dye in patients with macular hole, epiretinal membrane, or proliferative diabetic retinopathy/tractional diabetic macular edema. One surgeon performed standard chromovitrectomy and completed a postoperative questionnaire to compare the staining with that of the available dyes.

cid: a rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries.

cid is a computational tool developed in the Web environment to process cloned DNA fragments with the objective of masking the vector and adaptor regions, detecting the presence of microsatellites and designing the most appropriate primer pairs for the amplification of the identified repetitive sequences. This entire process is executed by the user in a simple and automated manner with the data input as a Zip file of chromatograms or a multiFASTA file. Thus, it is possible to analyse dozens of sequences at the same time, optimizing data processing and the search for the information of interest.