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Update README.md
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matsikora authored Jul 31, 2021
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Expand Up @@ -27,7 +27,7 @@ tion sites:
In addition, A_463.pdb,... and A_463.xtc,... files are created, each containing protein struc-
ture and a given number of glycan conformers, which can be readily visualised e.g. using
VMD:
<img src="TUTORIAL/IMG/tut1.svg.png">
<img src="TUTORIAL/IMG/tut1.svg.png" width="500">
If multiple conformations of the same protein are available, GlycoSHIELD can be used to
estimate the entropic cost of geometrically blocking certain glycan conformers in each protein
conformer. An artificial trajectory EC4_EC5.xtc with corresponding PDB file EC4_EC5.pdb
Expand Down Expand Up @@ -72,7 +72,7 @@ python GlycoSASA-0.1.py --pdblist A_463.pdb,A_492.pdb,A_533.pdb --xtclist A_463.
```
This will use 1172 conformers of each glycan to calculate the shielding score. As an output,
user obtains a plot of shielding score along the protein sequence:
<img src="TUTORIAL/IMG/tut4.svg.png">
<img src="TUTORIAL/IMG/tut4.svg.png" width="500">
In addition, a PDB file is created named “maxResidueSASA_probe_0.14.pdb”, where shield-
ing has been encoded in the column holding the beta factor information. Here, 0.14 denotes
the probe radius used for SASA calculation. An occupancy value of 1 marks residues acces-
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