Rationale: Complete final version of abstract and continue to accumulate data

Process:

• Lathan had commented that the RMSD (root mean square deviation) values for comparing tertiary protein structures were not very meaningful so I looked into another way to mathematically analyze the differences between the tape measure proteins (TMP)
• All of the structures had been folded by RaptorX so I started aligning them all in comparison to the NapoleonB TMP

Results:

• I found a paper that said that the TM-score is the best way to compare protein structures because it is independent of protein length. The tape measure proteins vary greatly in size so this is necessary to reduce error.
• TM-align also gives a TM-score with its results (it is actually the main poi for the software) so it was an easy switch over.
• Began to organize results in a tabular manner:

phage name	residues	residues in common	RMSD of common residues	TM-score	notes	image
Anansi	1432	1356	78.945	0.1524	random structural similarity
Andrew	787	787	40.957	0.1597	random structural similarity
Atraxa	616	616	29.188	0.1309	random structural similarity
BeautusComedenti	1029	1029	28.36	0.2266
BossLady	876	876	48.243	0.1695
Cheesy	1492	1492	49.672	0.2379
Chubster	1180	1180	41.169	0.2402
Constance	1298	1298	56.792	0.1247	random structural similarity
Corgi	555	555	34.341	0.0913	random structural similarity
DrManhattan	744	744	31.479	0.1715
EdgarPoe	1113	1113	27.514	0.2428
ElephantMan	1463	1427	24.285	0.368
Elesar	1607	1493	47.103	0.1432	random structural similarity
Faja	1348	1348	48.361	0.1552
Galaxy	793	793	32.454	0.1618
Gorgeous	1432	1356	79.112	0.1528
Hestia	1325	1325	43.792	0.153
Joann	853	853	29.797	0.1764
KellEzio	1029	1029	44.416	0.1805
KitKat	1029	1029	28.965	0.2266
Laila	665	665	34.138	0.1063
Laroye	946	946	25.419	0.2367

Next Steps:

Continue aligning stuctures and then use the data to create a figure.