Short Course 2 – Experimental Design and Analysis of Molecular Dynamics Simulations Applied to Drug Discovery
Trainer: Dr. Hugo Verli, Federal University of Rio Grande do Sul (UFRGS).
Dr. Hugo Verli
He has been a Professor at the Federal University of Rio Grande do Sul since 2006 and a Full Professor at the same University since 2022. He was an affiliated member of the Brazilian Academy of Sciences (2012-2016), supervised around 40 postgraduate students, including master’s and doctoral students, and was associated with more than 100 publications of full papers in scientific journals. He obtained around 2,500 citations in these works, reaching an H index of 29 by WoS and 37 by Google Scholar. He was coordinator of the Postgraduate Program in Cellular and Molecular Biology (PPGBCM) of the Center for Biotechnology at UFRGS, concept 7 in the CB1 area of CAPES between 2020 and 2023. He is currently vice-director of the Center for Biotechnology at UFRGS. He has experience in the area of Structural Bioinformatics, with emphasis on Molecular Simulation, working mainly on the following topics: dynamics of biomolecules, parameterization of bioactive compounds for molecular mechanics calculations, structure and dynamics of carbohydrates, glycoconjugates and their complexes. Member of the National Institute of Science and Technology in Childhood Cancer Biology and Pediatric Oncology – INCT BioOncoPed.
Description
The use of molecular dynamics (MD) simulations has become increasingly accessible to medicinal chemists, driven by the growing availability of supercomputing resources, software optimization, and the development of new methodologies. This progress has reshaped how computational experiments are designed and executed, enabling users to obtain more reliable, reproducible, and closer to benchwork results. However, despite the rising adoption of MD simulations in medicinal chemistry publications, methodological standards often fall short of the state-of-the-art in the field. This course aims to guide early-career researchers in designing and analyzing MD-based experiments, covering current best practices (e.g., replica simulations, control runs, statistical analyses including Markov State Models, enhanced sampling integration, and ligand-receptor affinity/stability predictions) as recommended by journals like the Journal of Chemical Information and Modeling. By doing so, we hope to elevate the scientific rigor of MD applications within our community and train the next generation of researchers.
Target Audience
Graduate students with basic knowledge of molecular dynamics.
Number of Available Slots
50 (room Armação).