Alignment by hand - Transfer of information

4 important questions on Alignment by hand - Transfer of information

When are residues likely to have the same physico-chemical properties?

When they sit at similar positions in similar structures

Do helices have one hydrophobic and one hydrophilic side?

Yes, but only if the pack one side against something

What does protein threading mean and when do you use it?

You drag the sequence step by step through each location on the template, you use it when you have a low sequence identity
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What are 3 ways to optimize alignments?

1. Use secondary structure preferences
2. 3D structures info
3. Multiple alignments

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