New course for 2010

Course Description

This course provides an introduction to the fundamentals of molecular design and analysis with an emphasis on the interactions between proteins and ligands.  Participants will visualize molecules and prepare protein/ligand complexes for molecular modeling.  They will modify a protein structure by mutations, insertions and deletions.  Finally, they will compare proteins by aligning sequences and structures.

Who Should Attend

Researchers who want to model proteins, and examine their interactions with ligands. People who want to take additional training courses that make use of proteins.

Requirements

Course participants should be familiar with basic manipulation of molecules and files in SYBYL-X.  These topics are covered in the course Getting Started with SYBYL-X.

What You Will Learn

• Produce mutated proteins with inserted or deleted residues.
• Create pictures that convey instant information.
• Communicate the important details of protein structure.
• Rapidly identify and fix problems in protein structure.
• Produce good protein geometries.
• Make efficient use of energy minimization in proteins.
• Assess protein similarities/differences using sequence alignments.
• Align protein structures for effective visual communication.
  

Course Topics

Course Objectives

1. Complete protein structure by adding sidechains, terminal groups and hydrogens.
2. Choose appropriate settings for staged minimization of protein energy.
3. Modify a protein structure, for both single-point mutations, and insertions or deletions.
4. Render a protein in a fashion that conveys structural information.
5. Create views useful for determining receptor-ligand interactions.
6. Define sets of atoms and residues that line the receptor cavity.
7. Align sequences for multiple proteins and determine the pairing of important residues.
8. Align a series of related proteins, and identify residues with differences in geometry (backbone and sidechain).

Modules Used

SYBYL-X (Biopolymer and MOLCAD).

Course Length

1 Day

Pricing Information

Tripos, Inc. reserves the right to modify course content at any time without prior notice.