This talk will focus on our group's efforts to develop and test new computational algorithms and protocols for de novo design termed NOVA (Navigation and Optimization for Virtual Assembly), and evolution-based searching termed CONGA (Construction by Genetic Algorithm), as an alternative to virtual screening in DOCK6.  Potential advantages (pros) and disadvantages (cons) for the three different techniques, as well as ease of setup and use will be discussed.  For simplicity, all three methods were incorporated into a single executable and use standard DOCK6 formats and input parameter files.  Each of the procedures can also use new similarity-based scoring functions we developed to help bound the search space during sampling (virtual screening) or chemical searching (de novo design, genetic algorithm).  Application examples using the different algorithms will be presented for several ongoing projects in our laboratory that are targeting HIVgp41, fatty acid binding protein, and zika glycoprotein E. <br/>

Virtual screening, de novo design, and evolution-based searching with DOCK

256th National Meeting (2018)

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