Table 8. The most possible folding conformations of PFVM-01. Left column
listed the UniprotKB and protein name; right column listed the PFVM-01
which is the PFSC string on top of PFVM. The PFVM of SUMO1_HUMAN is at
Table 1; the PFVM of P53_HUMAN at Table 3 and the PFVM of
K4GSD6_9SAUR, C4IXC1_9TELE, A0A851ZE52_9AVES and EP3B_HUMAN in
supplementary document.
With PFVM-01, the protein 3D structure can be constructed which
represents the predicted structure. The PFVM-01 is a PFSC string, which
represented the folding conformation for a protein. First, with
searching for similar conformations, an initiative 3D structure can be
constructed according an entire PFVM-01. Using high throughput screening
PDB, the similar structural conformations can be obtained according
folding similarity score with comparison between the PFVM-01 and all
PFSC strings in database. Thus, the initiative 3D structure can be
constructed according the 3D structure with highest folding similarity
score. Second, the parts of PFVM-01, particularly tertiary fragments,
can be further searched to improve 3D structure. Third, the side chains
are added for each residue. Finally, the constructed 3D structure is
optimized by computed for free energy minimization. With PFVM-01, six of
3D structures are predicted and displayed in Figure 5. First row
displays the predicted 3D Structure from PFVM-01 of SUMO1_HUMAN; second
row displays the predicted 3D Structure from PFVM-01of P53_HUMAN. The
SUMO1_HUMAN and P53_HUMAN have the known 3D structures, so the
comparison between known 3D structure and the predicted structure (in
brown color) are shown on left side. Although proteins of K4GSD6_9SAUR,
C4IXC1_9TELE, A0A851ZE52_9AVES and EP3B_HUMAN do not have 3D
structures available in PDB, their most possible 3D structures can be
predicted by PFVM-01 are displayed respectively in Figure 5.