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

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

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

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

Preparing a raw PDB file containing a Protein-Protein complex

This video shows how to prepare a raw PDB file containing a Protein-Protein complex (no small molecules present) for use in MOE...
Oct-18-2023

Preparing a raw PDB file containing multiple ligands

This video shows how to prepare a raw PDB file containing more than 1 ligand for use in MOE for tasks such as interactive analy...
Oct-18-2023

Preparing a raw PDB file for use in MOE

This video shows how to prepare a raw PDB file for use in MOE for tasks such as interactive analysis or Docking. [link]video....
Oct-18-2023