Section: Research Program

As-Rigid-As-Possible methods for molecular paths

Last year, in the scope of Minh Khoa Nguyen's PhD, we have adapted the As-Rigid-As-Possible (ARAP) paradigm used in Computer Graphics to generate paths of molecular systems. This year, we continued this line of research with new extensions of the ARAP methodology. One extension led to generate conformational transition paths with low potential-energy barriers for proteins. It was published to the Journal of Computer-Aided Molecular Design, 2018 [66]. Another extension concerned the ART-RRT method which incorporates the ARAP methodology inside tree-based exploration methods to approximate ligand unbinding pathways. This contribution was published to the Journal of Computational Chemistry, 2018 [65]. Finally, the PhD thesis of Minh Khoa Nguyen titled Efficient exploration of molecular paths from As-Rigid-As-Possible approaches and motion planning methods was defended in March 2018 [67]. A brief summary of the above-mentioned contributions is presented below.