38th Molecular Modeling Workshop 2026

Schrödinger is excited to be participating in the 38th Molecular Modeling Workshop 2026 conference taking place on March 9th – 10th in Erlangen, Germany. Join us for a presentation and workshop by Jonas Kaindl, Principal Scientist I at Schrödinger.

Workshop: More than moving pictures: Molecular Dynamics with Desmond

Speaker: Jonas Kaindl, Principal Scientist I at Schrödinger

Abstract: If you’re interested in running molecular dynamics simulations in your research, in this workshop you can learn how to run MD simulations with the Schrödinger suite. We’ll use two examples, a small molecule ligand in water and a protein-ligand complex, and look at how to prepare the structures and set up the simulation. Once the simulation is completed, we’ll go through different methods to analyze trajectories in Maestro, including analyzing RMSDs, occupations, solution phase conformers, solvation patterns and other interesting properties.

Preparation:

Every participant is required to download the Schrödinger license and bring their own laptop with the Schrödinger suite installed. Since we will not go through the basic functionalities of Maestro, we strongly encourage participants to go through our “Getting going with Maestro” section on our website to learn the basics (requires a free website account): Getting going with Maestro

Should you wish to prepare further, here are additional resources:
Learning Paths for Small Molecule Drug Discovery
Introduction to Structure Preparation and Visualization

Presentation: Let it go: exploring and learning from unbinding pathways

Speaker: Jonas Kaindl, Principal Scientist I at Schrödinger

Abstract: The estimation of drug-target residence time has been widely adopted in drug discovery and lead optimization campaigns as a metric to control and modulate in vivo drug efficacy. Over the years, several computational approaches have been developed to simulate unbinding kinetics and calculate dissociation rates. In addition to accurately predicting residence time, understanding the molecular basis of the unbinding event is crucial to support and drive the design of drugs with optimized kinetic profiles. Here, we present the application of the unbinding kinetics workflow developed by Schrödinger to accurately predict the residence time and to study the unbinding mechanism of a set of drug-target systems [1]. We applied the presented approach to different target classes and modalities, looking at the details of the dissociation process and understanding the determinants of such an event. Overall, the results demonstrate the applicability of the workflow in assisting drug design with minimal human intervention and a computational cost compatible with drug design cycle timeline.