Peptide Modeling

Interactive Structure-Based Peptide Optimization

This video covers MOE applications for interactive structure-based design, including active site visualization, protein-peptide...
Oct-18-2023

Finding key contacts for a protein-protein interface using Protein Contacts

This video shows how to analyze key contacts between; a protein–protein interface, for a given loop or region, or a specific re...
Oct-18-2023

Modeling Cyclic Peptides with MOE

Cyclic peptides have long been of interest as potential therapeutics, but these “big small molecules” present many challenges f...
Dec-18-2023

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

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

Analyzing and comparing Protein-Ligand complexes using Ligand Interactions

This video shows how to generate a Ligand Interaction diagram for identifying key interactions, steric fit, potential binding o...
Nov-21-2023

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

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

Computing molecular properties for a database of small molecules using Calculate Descriptors

This video shows how to compute molecular properties for a database of molecules for tasks such as filtering, building QSAR mod...
Nov-21-2023