Chem 110L: Macromolecular Visualization Laboratory Exercise: Concluding Remarks
SYBYL and PyMOL: Concluding Remarks
In the first part of the tutorial you became familiar with the modeling and visualization program SYBYL. The richness of functionalities in SYBYL makes it a valuable program for solving many biochemical problems in silico. For example, researchers in pharmaceutical industry use SYBYL to find drug molecules that best fit into the enzyme's active site, and researchers at universities use SYBYL to model how proteins fold into their native three-dimensional structures. Some other tasks that you can perform with SYBYL include:
- Build small molecules from scratch
- Build protein and DNA structures based on the sequence
- Combine molecules from different files into one complex
- Separate complex of molecules into individual components
- Alter the chemical structure of proteins by changing one amino acid into another
- Find low-energy conformations of molecules
- Calculate atomic charges and dipole moments of molecules
- Calculate and display molecular orbitals
In the second part of the tutorial you learned some of the capabilities of a powerful visualization program PyMOL. You saw that it offers great control on how things are being displayed, and can generate nice ray-traced images for scientific publications. Some other tasks that you can perform with PyMOL and its plug-ins include:
- Measure distances, angles, and dihedral angles and show hydrogen bonds
- Apply crude mechanical force to alter the structure of macromolecules, e.g. wrap a DNA strand around a cluster of metal atoms; this is called sculpting
- Identify surface cavities that can act as binding pockets for ligands
- Edit structures by creating and breaking bonds or rotating groups around single bonds.
- Alter the chemical structure of proteins by changing one amino acid into another, and find the optimal position for the mutated residue.
- Find low-energy conformations of molecules
- Calculate atomic charges and dipole moments of molecules
- Calculate and display molecular orbitals
You will have a chance to learn more about the advanced capabilities of these programs in other biochemistry courses.
>