Protein, DNA/RNA Modeling

Using Surface and Maps to Understand Properties and HotSpots

This video shows how to generate visual representations of molecular surfaces and hotspots with examples applied to a protein-l...
Feb-09-2024

Building molecules using the Protein Builder

This video shows how to build a peptide from scratch; mutating residues, control backbone geometries, repacking and exploring r...
Feb-01-2024

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

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

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

Protein Surface Charge and Hydrophobic Patch Analysis

Protein patch analysis is a computational method for identifying and assessing protein interaction hot spots which may be impli...
Nov-21-2023

Creating and Analyzing Focused Mutant Libraries for Protein Engineering

Computational techniques for optimizing the affinity of a potential therapeutic protein or antibody are described. Experimental...
Nov-21-2023

Antibody Modeling and Developability Assessment

Antibody candidates often have poor biophysical properties and/or chemical liabilities that cause downstream developability iss...
Nov-21-2023

Protein-Protein Docking and Epitope Analysis

The MOE Protein docking application is used to map epitopes and other protein-protein interfaces (PPI). This automatically calc...
Nov-21-2023

Advanced Protein Alignment and Superposition

This video shows how to align and superpose multiple proteins, handle multiple chains, use dendrograms and other visualization ...
Oct-18-2023