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Changes for page MLCE - PPIs prediction

Last modified by emacasali on 2023/01/11 16:04
From version 14.1
edited by emacasali
on 2023/01/11 15:47
Change comment: Uploaded new attachment "image-20230111154750-1.png", version {1}
To version 25.1
edited by emacasali
on 2023/01/11 16:00
Change comment: There is no comment for this version

Summary

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18 18  
19 19  Mathematically speaking this process is an energy decomposition method, which starts with the calculation of the unbound part of the potential E (van der Waals, electrostatic interactions, solvent effects) through an MM/GBSA calculation:
20 20  
21 +(% style="text-align:center" %)
22 +[[image:image-20230111154750-1.png||height="263" width="536"]]
21 21  
22 -= Who has access? =
24 +Since the first eigenvector contains most of the relevant energy information about the interactions in the system, we can approximate the matrix energy to the first eigenvector:
23 23  
24 -Describe the audience of this collab.
26 +(% style="text-align:center" %)
27 +[[image:image-20230111154917-1.png||height="47" width="225"]]
28 +
29 +Finally, we can filter the approximated interaction matrix Mio for residues that are in geometric proximity in the structure (closer than 6Å):
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31 +(% style="text-align:center" %)
32 +[[image:image-20230111155023-1.png||height="48" width="253"]]
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35 += How to use the script =
36 +
37 +Please see the attached documentation files in Drive repository.
38 +
39 +
40 += References =
41 +
42 +~1. Scarbelli, G.; Morra, G.; Colombo, G., Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping, Biophys. J., 2010, 98, 1966, [[https:~~/~~/doi.org/10.1016%2Fj.bpj.2010.01.014>>https://doi.org/10.1016%2Fj.bpj.2010.01.014]]
43 +
44 +2. Genoni, A.; Morra, G.; Colombo, G., Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions, J. Phys. Chem. B, 2012, 116, 10, 3331–3343, [[https:~~/~~/doi.org/10.1021/jp210568a>>https://doi.org/10.1021/jp210568a]]
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25 25  )))
26 26  
27 27  
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31 31  {{toc/}}
32 32  {{/box}}
33 33  
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34 34  
35 35  )))
36 36  )))
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