Modeling with cryo-EM

This tutorial covers the use of MODELLER to build complete 3D models of an 'unknown' protein structure (i.e. not solved by X-ray crystallography) given three sources of experimental information:

• The amino acid sequence of the unknown protein structure.
• The PDB database of other, known protein structures.
• A cryo-EM map of the unknown protein structure.

In order to follow through this tutorial, the input files must first be downloaded. These files are available as a compressed archive in both .tar.gz (for Mac or Linux) and zip (for Windows) format (the same files are contained in each format archive). The archive contains a subdirectory for each step in the tutorial, and each step in turn contains a results subdirectory containing sample results from running the scripts.

The protein used in this example is a novel gene for lactate dehydrogenase that was identified from the genomic sequence of Trichomonas vaginalis (TvLDH). For some other sample studies with this system, please refer to the regular MODELLER tutorial.

• Step 1: Search for suitable templates
• Step 2: Select a template
• Step 3: Align sequence with structure(s)
• Step 4: Build comparative models
• Step 5: Assess the quality of the models
• Step 6: Fit models into cryo-EM maps
• Step 7: Refine models with loop modeling
• Step 8: Flexible cryo-EM fitting with Flex-EM