Rescoring is a simple approach that theoretically could improve the original docking results. In this study AutoDock Vina was used as a docked engine and three other scoring functions besides the original scoring function, Vina, as well as their combinations as consensus scoring functions were employed to explore the effect of rescoring on virtual screenings that had been done on diverse target...

Bacterium Pseudomonas aeruginosa is a human opportunistic pathogen. It can cause infection of immunocompromised people or people suffering from cystic fibrosis, which is often fatal. Bacterial colonization of human tissues is mediated by interaction of bacterial surface proteins – lectins – with cellular surface carbohydrates. PA-IIL is Pseudomonas aeruginosa tetrameric lectin, which contains t...

For my course project I chose to explore docking software and its application to virtual screening. While there are many good reviews in the literature on docking software (e.g. Schneider, 2002), I wanted to supplement this material with some firsthand experience. I was able to gain access to three commercial docking programs, and while the software is both sophisticated and complex, was able t...

Flaviviral infections affect millions of people throughout the world, in such different territories as Europe, Australia, USA, and China. Among these infections are dengue fever, tick-borne encephalitis, Powassan encephalitis, West Nile fever, yellow fever, Omsk haemorrhagic fever, etc. Effective vaccines exist against only several flaviviruses. Moreover, there is no other specific therapy for ...

Neonatal diagnosis of congenital toxoplasmosis is based on a combination serological and molecular tests. Maternal screening treatment differ according to national policies may impact the sensitivity diagnostic methods in infants at birth.

The machine learning-based virtual screening of molecular databases is a commonly used approach to identify hits. However, many aspects associated with training predictive models can influence the final performance and, consequently, the number of hits found. Thus, we performed a systematic study of the simultaneous influence of the proportion of negatives to positives in the testing set, the s...

High throughput screening (HTS) involves using automated equipment to test a large number of samples against a defined molecular target to identify a reasonable number of active molecules in a timely fashion. Major factors which can influence priorities for the limited resources of the HTS group are projects, productivity, progress and people. The challenge to the HTS group is to provide excell...

We present the discovery of innovative low molecular weight inhibitors against human immunodeficiency virus 1 (HIV-1) protease. Structure-based virtual screening focused on potential allosteric surface cavities revealed these compounds [1]. To identify and prioritize such cavities we performed a molecular dynamics simulation were we concentrated on flexible and transient potential binding sites...

Metallo-β-lactamases can hydrolyze a broad range of β-lactam antibiotics and no effective inhibitors could be used in the clinic. Therefore, the discovery of metallo-β-lactamase inhibitors has attracted much attention in recent years. In this study, a support vector machine (SVM) that separates compounds into positives and negatives, combined with docking method was employed for virtual screeni...