Table 1. Summary of structural modelling studies in chronological order.
From left to right, the columns are the names of the authors, year of publication, algorithm of choice for template selection, number of templates used per query, algorithm used for modelling, algorithm used for model validation, algorithm used for model refinement, target/ antigen against which the VHH in the study is generated, name of the VHH used in the study, organism from which the respective VHH is synthesized and PDB ID of the template(s) used in the study.
| Authors | Year | Template selection | Templates/query | Modeling methods | Antigen | VHH (main study) | Template(s) |
|---|---|---|---|---|---|---|---|
| Smolarek et al. | 2010 | PSI-BLAST against PDB | one | Modeller | DARC- C terminus | CA52 | 1OP9 and 1 JTO |
| Govaert et al. | 2011 | mutation studies | not applicable | Esypred3D,Robetta for mutants | not applicable | cAbAn33, cAbLys3, and cAbPSA-N7 | not mentioned |
| Sircar et al. | 2011 | BLAST | one or many | Rosetta Antibody VHH suite | not applicable | not applicable | not applicable |
| Chavanayarn et al. | 2012 | BLAST | one | not mentioned | Phospholipase 2 of Naga koultia | P3-1, P3_3 | 1VHP and 1MVF |
| Thueng-in et al. | 2012 | BLAST | one | not mentioned | NS5B(RNA dependent RNA polymerase) of hcv | VHH6, VHH24 (clone names) | 1VHP, 1F2X |
| Phalaphola et al. | 2013 | BLAST | one | not mentioned | NS3-C ( HCV helicase) | VH6,VHH9,VH59 | 1OHQ,1XFP,3BN9 |
| Inoue et al. | 2013 | not mentioned | one | MOE (CCG) | Hen Egg White Lysozyme | cAb-CA05-(C-C-L), cAb- CA05-(#16-#09-L), cAb-CA05-(#16-#19-L) | 1RI8 |
| Hoseinpoor et al. | 2014 | PSI-BLAST ( Phyre2) | one | Phyre2 | H.pylori Urease | HMR23 | not available |
| Steeland et al. | 2015 | not mentioned | multiple | swiss model server | TNF receptor 1 | Nb70 and Nb96 | 4FZE, 4JVP, 3P0G, and 2KH2 |
| Shirin Shahangiana et al. | 2015 | BLAST against PDB | one | Modelller 9.13 | VEGFR | VEvhh1, VEvhh2, VEvhh3 | 1OP9-A , 1MVF-A and 2X6M-A respectively |
| Jittavisutthikul et al. | 2015 | i-TASSER | not mentioned | I-TASSER and ModRefiner | NS3/4A | VHH24, VHH28, VHH41 | not mentioned |
| Unger et al. | 2015 | BioLuminate suite | multi (different for frs and cdrs of each vhh) | BioLuminate | CDTa/b( clostridium difficile toxin a/b) | 1+8, 1-14, 1+18 (3 VHH clones) | numerous |
| Fridy et al. | 2015 | based of target- IgG complex PrA1-Fab | one | I-TASSER | not mentioned | LaP-1 to 4 | not mentioned |
| Calpe et al. | 2015 | BLAST | one | Modeller | Bone Morphogenic factor 4 (BMP) | C4, E7, C8 | 4BSE, 1SJX |
| Prado et al. | 2016 | BLAST against PDB | one | Modeller 9.10 | BthTX-I and BthTX-II | KF498607, KF498608, KC329715 and KC329718 | 4KRP-B, 4DKA-A, 3EZJ-B, 4KRP-B |
| Jullien et al. | 2016 | Discovery studio | one | Modeller 9.10 from Accelrys Discovery Studio v. 3.1 (DS 3.1) | Histones 2A and 2B | nabobody against chromatin (Chromatibody) | 4IDL |
| Demeestere et al. | 2016 | Swiss model web server | multiple | Modeller | Matrix metallo proteinases 8 | Nb14 | 4LAJ, 3EZJ, 3TPK and 4M3J |
| Se et al. | 2016 | PS2V2 server | one | Modeller through PS2V2 server | Bap protein Acinetobacter baumanii | VHH1 | 1MVF |
| Leem et al. | 2016 | BLAST | many | Modeller and FREAD (for CDR loop prediction) | not applicable | not applicable | not applicable |
| Soler et al. | 2016 | Pre existing knowledge | many | Swiss Model server | lysozyme | NbHuL6, cAbLys, cAbCII10 | NbHuL6-3EBA and 3DWT, cAbLys and cAbCII10 1ZMY, 1JTP |
| Malik et al. | 2016 | ”best fit structures” | one | Raptorx | CyaA-RTX Segment | VHH2,VH5,VH18,VHH37 | 1F2K,4O9H,2KH2,4HEP |