2021 Denovo tutorial 1 with PDBID 1HW9

In this session, we are going to use the predetermined structures from the virtual screen tutorial to do de novo design

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I. Focused De Novo Design

In the focused De Novo Design, we will generate the same ligand present in the structure by connecting fragments from scratch. Putting the generated fragments back into the pocket, we could check how our simulation works in terms of the protein we are interested in

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Fragment Libraries

First, a focused fragment library will be generated based on the original ligand. The fragments would build the same ligand in an atomic structure.

Create a new directory for the fragment library, use the command:

mkdir 010_dn_fraglib

Create a new input file for fragment generation, use the command:

touch fragment.in