The journey of a cheminformatics scientist
I recently finished my PhD in Cheminformatics (from the Department of Chemistry) at North Carolina State University. I worked on my PhD for three and a half years; I started it in August 2016 and defended on March 24th 2020. During that time, I published five articles (three as first author), one article is currently…
Today, I want to write a tutorial on how to generate chemical space visualizations using a combination of R and Gephi. I have found them to be a powerful way of assessing the chemical data and finding hidden patterns that could be crucial in estimating the biological endpoints of interest. Before we go on, let…
Are you tired of creating one molecule at a time using Marvin View? I know the struggle. My folder was overflowing with individual molecule files, and it was becoming a nightmare to efficiently dock them against my target protein. But fear not, because I have found a solution, with the help of a research member…
Abstract We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME (freely available in github) can enumerate fully assembled macrolides with synthetic feasibility by utilizing the constitutional and structural knowledge extracted from biosynthetic aspects of macrolides. Taken into account by the software are key information such as…
Abstract We report on the development of a cheminformatics enumeration technology and the analysis of a resulting large dataset of virtual macrolide scaffolds. Although macrolides have been shown to have valuable biological properties, there is no ready–to–screen virtual library of diverse macrolides in the public domain. Conducting molecular modeling (especially virtual screening) of these complex molecules is…