Overview In this exercise, we will: Download a PDB structure of a mutated protein. In its native state, the protein is glycosylated, and it does not perform its functions properly without at least some of the glycosylation. Use the text editor and the utilities at GLYCAM-Web to change the mutated residues back to the natural […]
Overview GLYCAM-Web provides tools to facilitate molecular modeling of oligosaccharides and larger molecular structures containing glycans. Type ‘legacy.glycam.org’ (or ‘http://legacy.glycam.org’) to go there. You should see a page looking like the one just below. Once there, click on 3D Structure Prediction Tools, the gray tab on the left near the top. You should now […]
Determining the ring conformation of Iduronic acid from a PDB file using BFMP. If needed, please click here for instructions on downloading and installing the BFMP program. The program requires two input files: a text file in PDB format and a configuration file. Click here to download BFMP-Tutorial2.tar.gz, the input and output files for this tutorial Using vi or […]
Determining the ring conformation of A-L-Idopyranose during the course of a 10ns MD simulation using BFMP. If needed, please click here for instructions on downloading and installing the BFMP program. The program requires three input files: an AMBER format topology file, AMBER format trajectory file and a configuration file. Click here to download BFMP-Tutorial1.tar.gz, the Input AMBER format files and output […]