Using molecular dynamics to produce an ensemble of protein conformations for more biologically relevant docking experiments


Date: Thursday 6th April, 2023

Time: 2pm GMT / 3pm CET / 9am EST

Duration: 45 minutes

Format: Webinar


Docking is a method that utilizes protein structures to generate ligand binding poses and scores the interactions that are made. This method is used extensively in drug discovery to screen molecule designs and help prioritize them. Docking software typically treats the protein as a rigid body, whilst the ligand is conformationally flexible. Occasionally this is problematic because the protein structure is not in the biologically relevant conformation for a given ligand, which leads to the docking results not being relevant. In this case study, we will firstly validate the approach of using molecular dynamics (MD) to produce an ensemble of protein conformations to be used with ensemble docking in Flare.

About the presenters

Abhi Kayal 

Abhi_Kayal_Author-ImageAbhijit Kayal completed his PhD in Computational Chemistry at the Indian Institute of Technology
Kanpur, India. He then joined Juelich Research Centre Germany for postdoctoral studies. After that, he joined Quantumzyme Bangalore, India as a scientist and his work primarily focused on computational enzyme engineering. Abhijit’s experience spans in silico enzyme modeling by using different computational approaches. As an Application Scientist at Cresset Abhijit’s responsibilities includes training and supporting customers, enabling them to achieve their scientific goals through the use of Cresset’s ligand-based and structure-based software solutions.

Rick Hara 

Ryuichiro Hara (Rick) completed his PhD in Synthetic Chemistry at the University of Tokyo and Graduate
School of Advanced Studies, Japan. 650x650_RickHe studied synthetic and coordination chemistry at the Institute for Molecular Science, Hokkaido University and MIT. His studies then diverted to database theory and image processing technology on IC, whilst teaching at the Kanazawa Institute of Technology and helping Morpho,
Inc. Using these two areas of excellence, he is highly motivated in offering a variety of technologies to customers seeking new methods in the field of drug discovery.