MOLECULAR MODELING WORKSHOP FOR LIFE SCIENCE APPLICATIONS

Aug 15 - 16, 2002

Rm. 151, Noyes Lab, UIUC

Accelrys Inc (formerly MSI Inc) will be holding an advanced molecular modeling workshop for life science applications. It uses exclusively the InsightII interface and is organized for the beginning user (see detailed agenda below). From visualization through building to advanced molecular docking techniques, this workshop introduces the student to molecular modeling and protein/ligand interactions. Prior modeling experience is not assumed.

During the two-day workshop each unit consists of an applications lecture followed by a hands-on session during which attendees can follow suggested tutorials and projects. Time is usually available to discuss application of the techniques learned in the workshop to the attendees’ research.

Attendance for the workshop is free but limited to groups participating in the Accelrys/MSI software program. Registration is required. Limit of one member per group.

For information about registration please contact:

Dr. Jerome Baudry

Research Scientist

Rm. 150, Noyes Lab

Tel: 244-3210

Email: jerome@scs.uiuc.edu

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Workshop agenda:

LIFE SCIENCE WORKSHOP:

Introduction to InsightII and Docking

As a prerequisites, users must be familiar with basic UNIX commands.

Day 1:

9:00 ? 9:15 Welcome and Administration Announcements

9:15 ? 9:45 Introduction to Molecular Modeling (Lecture)

9:45 ? 11:00 Visualization Exercises (Lab)

Lesson 1: The Basics of Insight II (Viz1)

Lesson 2: Visualizing Molecules (Viz2)

Lesson 3: Annotation and Images (Viz3)

11:00 ? 12:00 Building Molecules (Lecture)

1:00 ? 2:00 Building Molecules (Lab)

Lesson 1: Using the 2D Sketcher (Build1)

Lesson 2: Building in 3D (Build2)

Lesson 3: Building Peptides (Build3)

Lesson 4: Preparing a PDB File for Molecular Mechanics (Build4)

2:00 ? 3:00 Force Fields and Energy Minimization (Lecture)

3:00 ? 3:45 Conformational Energy (Lab)

Lesson 1: Minimization Using CHARMm (Mini1)

Lesson 2: Step-Wise Minimization of a Protein (Mini2)

3:45 ? 4:15 Conformational Searches and Molecular Dynamics (Lecture)

4:15 ? 5:00 Conformational Searches and Molecular Dynamics (Lab)

Lesson 1: Restrained Molecular Dynamics (MD1)

Lesson 2: Dynamics of a Protein-Ligand Complex (MD2)

Lesson 3: Systematic Conformational Searches (MD3)

Day 2:

9:00 ? 9:45 Identification of Binding Sites (Lecture)

9:45 ? 11:00 Identification of Binding Sites (Lab)

Lesson 1: Binding Site Search Using Binding Site Analysis (ID1)

Lesson 2: Binding Site Search Using Evolutionary Trace (ID2)

Lesson 3: Template-Based Search with SH2 Domains (ID3)

Lesson 4: Template-Based Search on Aspartic Proteases (ID4)

11:00 ? 12:00 Characterization of Binding Sites (Lecture)

1:00 ? 2:00 Characterization of Binding Sites (Lab)

Lesson 1: Initializing and Running an MCSS Search (Char 1)

Lesson 2: Analyzing the Results of an MCSS Search (Char 2)

Lesson 3: De Novo Inhibitor Design for the SH2 Domain (Char 3)

2:00 ? 2:30 Docking: Manual and Automatic Methods (Lecture)

2:30 - 3:00 Docking (Lab)

Lesson 1: Monitoring Interactions during Manual Docking (Dock1)

Lesson 2: Automatic Docking with Affinity (Dock2)

3:30 ? 4:30 Lead Optimization (Lecture)

4:30 ? 5:00 Lead Optimization (Lab)

Lesson 1: OPPA Ligand Design (OPT1)

Lesson 2: Ligand Optimization with LUDI (OPT2)