Conformational states of Wilbrand's famous aromatic hydrocarbon at 568.15K

"Hands-On" Workshop for Accelrys' Insight II Molecular Modeling Application

The workshop will take place on Thursday May 18 from 10:00AM to 3:00PM and be held in the Engineering building room 220.

Workshop Agenda

10:00 AM - 10:30 AM Welcome

Welcome and introductory remarks by instructors Namita Patel and Christopher Paolini

10:30 AM - 12:30 PM Basic usage of Insight II

• Logging into and out of the Linux workstation for direct access to Insight II

• Using X-Win32 to access Insight II remotely from a PC running Windows NT/2000/XP

• Overview of Unix/Linux file system operations using GNOME and the shell (command line interpreter)

• Launching and closing Insight II

• Overview of folder operations in Insight II

• Downloading and importing protein data bank (PDB) and MOL model files

• Overview of Insight II mouse functions

• Model visualization operations: slab pose, world scale, X-, Y-, Z-rotation and translation, rendering styles (CPK, surface, secondary structure, ribbon)

• Molecule operations: Color Command, Label Command, Display Molecule, measurement functions (Distance, H-Bond, Angle)

• Overview of Insight II Modules: Builder, Biopolymer, Discover, Docking

• Hands-on example: building and modifying a peptide structure using the Biopolymer module

• How to superimpose two structures

• How to save, restore and remove molecular structures

12:30 PM - 1:30 PM Break for lunch

1:30 PM - 3:00 PM Using the minimization and dynamics capabilities of Insight II

• Overview of molecular minimization and numerical methods used by Insight II

• Hands-on example: construction of a simple aromatic compound using fragments from the hydrocarbon library

• Applying an energy potential function using the Forcefield facility

• Invoking an energy minimization operation using the Discover module

• Simulating molecular motion using the molecular dynamics facility

• Visualizing molecular motion: altering sampling frequency, colors, exporting to TIF and VRML formats, VRML applications

• Hands-on visualization and animation example: simulating the motion of a large dendritic polymer

• Using consensus restraints to identify structural similarities among a set of homologous compounds

• Hands-on example using consensus dynamics to aid in chemical similarity searching: using restraints to identify a set of structures of several inhibitors of angiotensin-converting enzyme in which a specified pharmacophoric area exhibits an equivalent conformation

• Closing remarks and free time for students to experiment with Insight II