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.