A typical medicinal chemist research scenario involves more and more 3D molecular modelling. Current components utilized in visualization and manipulation of experimetal X-ray structures and small molecules will be demonstrated in a concept that can easily be applied by not only computational chemists but medicinal chemists as well.

1. 3D visualization for medicinal chemists
Timea Polgar, Miklos J Szabo
Adrian Kalaszi Andras Kovacs

3. Works for medicinal chemists
2D structure and derived properties 3D structure and derived properties
Status quo Quo vadis

4. In situ structure-based molecular design
Easy analysis of protein – ligand interaction
Interactive 2D view of binding mode
Ligand edited in 2D and displayed in 3D
N23
R154
G54

5. In situ structure-based molecular design
Easy analysis of protein – ligand interaction
Interactive 2D view of binding mode
Ligand edited in 2D and displayed in 3D

6. In situ web-based structure-based molecular design
Ligand
partial optimization
molecule dynamics
conformation analysis
Protein
side chain optimization
backbone optimization
active site molecule dynamics

7. MarvinSpace reloaded
file widget
file widget
Interactive WebGL-based protein visualizer
Server side component for geometry generation
Communication relies on simple http requests
Internet Explorer supported

8. What is so easy about it?
Drag & Drop
3D protein structures
2D and 3D small molecules

9. Compound design at medchems bench
Ligand – ligand alignment
Pharmacohopre perception
Ligand alignment within a pocket
Protein – ligand interaction
X-ray/NMR – ligand binding
Docking results from CompChem

10. Summary
3D visualization facilitating communication between medicinal
and computational chemists
Intuitive UI and web-based technology visualizing and
manipulating with 3D information
Try out at the Test Lab corner