Molecular Simulations

Free Energy Calculations with Thermodynamic Integration in MOE using AMBER

Until the advent of GPU-accelerated molecular dynamics, alchemical free energy simulations had not been routinely applied in ea...
Dec-18-2023

Mixed QM/MM Methods: MOE and ONIOM

Detailed understanding of electronic effects are critical for properly understanding enzymatic reactions, or processes that occ...
Dec-18-2023

Creating a storyboard and tracking design ideas using Capture

This video covers how to capture the contents of the MOE window (e.g., viewpoints, rendering, surfaces, ligand properties, and ...
Oct-24-2024

LowModeMD: Conformational Search of Macrocycles and Protein Loops

We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is...
Nov-21-2023

Revealing Conformational Behavior in Solution through NMR Data Analysis

A dynamic, small molecule ligand may adopt a range of conformations in solution compared to its constrained conformation when b...
Nov-21-2023

New and Enhanced Features in MOE 2024.06

CCG is pleased to announce the 2024 release of the Molecular Operating Environment, MOE. In this webinar we will present new fe...
Oct-03-2024

From Structure to Dynamics Simulation: Running & Visualizing MD Trajectories

Setting up a Molecular Dynamics simulation starting from a protein PDB structure can be challenging. It involves: data preparat...
Dec-18-2023

Performing Solvent Analysis on a Protein-Ligand Complex

This video shows how to use the Solvent Analysis tool, to predict the location and energetic favorability of water molecules in...
Oct-09-2024

Modeling Targeted Protein Degradation via Bifunctional Degraders and Molecular Glues

In recent years, targeted protein degradation has emerged as a new modality to control protein levels in vivo. Both heterobifun...
Dec-18-2023

Modeling Ternary Complexes with Molecular Glues: Making Sense of a Sticky Situation

Targeted protein degradation has emerged in recent years as a new modality to control protein levels in vivo. Among the many co...
Dec-18-2023