Modeller

Manufactured by Schrödinger

Sourced in Germany

The Modeller is a software tool designed for molecular modeling and simulation. It provides a platform for constructing, visualizing, and analyzing molecular structures. The core function of the Modeller is to generate 3D models of proteins, nucleic acids, and other biological macromolecules based on their sequence information or experimental data.

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Lab products found in correlation

Macromodel, by Schrödinger (3 mentions) Pymol 2, by Schrödinger (1 mentions) Piper, by Schrödinger (1 mentions) Sybyl x 2, by Certara (1 mentions) Gromacs, by Schrödinger (1 mentions)

6 protocols using modeller

Structural Impact of Protein Mutations

Cited 5 times

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Mutations can affect or disrupt protein structure and function. Computational structure-based approaches have been shown to be invaluable tools to unravel the molecular mechanism of mutations giving rise to a phenotype.^{38 (link)–41 (link)}In order to assess the structural effects of the mutation, the available X-ray crystal structure of the human STAG2 in complex with SCC1 was used (PDB ID’s: 4PJU, 4PJW, and 4PK7). Based on these structures, models of complexes of STAG2 with the other cohesin subunits SGO1 and WAPL were generated using Modeller^{42 (link)} and MacroModel (Schrodinger, New York, NY).
The effects of the mutations on protein stability and affinity for its partners were assessed in this work using two methods: DUET^{30 (link)} and mCSM-PPI.^{32 (link)} They represent a class of novel machine-learning methods that extract patterns from graph representations of the three-dimensional residue environment structure in order to quantitatively predict the effects of missense mutations on protein stability,^{30 (link), 32 (link)} protein–protein interactions,^{32 (link), 43} protein–nucleic acid interactions,^{30 (link)} protein small-molecule interactions,^{44 , 45 (link), 46 (link)} and protein–metal ion interactions.^{31 (link)}

Soardi F.C., Machado-Silva A., Linhares N.D., Zheng G., Qu Q., Pena H.B., Martins T.M., Vieira H.G., Pereira N.B., Melo-Minardi R.C., Gomes C.C., Gomez R.S., Gomes D.A., Pires D.E., Ascher D.B., Yu H, & Pena S.D. (2017). Familial STAG2 germline mutation defines a new human cohesinopathy. NPJ Genomic Medicine, 2, 7.

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Structural Modeling of Human DBR1

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Models of apo DBR1 and DBR1 in complex with RNA, comprising residues 2-349, were generated using Modeller41 (link) and MacroModel (Schrodinger, New York, NY) using the X-ray crystal structures of apo DCR1 (PDB code: 4PEF24 (link)) and in complex with a substrate analogue, synthetic RNA that mimics the RNA lariat branchpoint (PDB codes: 4PEH and 4PEI24 (link)) from Entamoeba histolytica (35% sequence identity with human DBR1). The models were then minimized using the MMF94s forcefield in Sybyl-X 2.1.1 (Certara L.P., St Louis, MO), with the final structure having more than 95% of residues in the allowed region of a Ramachandran plot. Following previous approaches42 (link)43 (link)44 (link), a manganese ion was manually added to the active site after comparison with the manganese-bound DCR1 structures indicated the conformation of residues in the manganese-binding motif were identical in the two proteins. The root mean square deviation (RMSD) between the models and the templates was 0.21–0.22 Å. The quality of the models was confirmed with Verify3D45 (link) (data not shown). Model structures were examined using Pymol.

Pires D.E., Chen J., Blundell T.L, & Ascher D.B. (2016). In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Scientific Reports, 6, 19848.

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Homology Modeling of Claudin Proteins

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Homology models were created utilizing MODELLER¹⁹ (link) and Schrödinger's BioLuminate/Maestro (Biologics Suite, Release 2019-2, Schrödinger, Germany). For the claudin-10b protomer model, the claudin-15 crystal structure²⁰ (link) (PDB ID 4P79) was used as template. For the claudin-10a protomer model, the claudin-10b model was used as template. Images were created with PyMOL 2.3 (Schrödinger, Germany).

Sewerin S., Piontek J., Schönauer R., Grunewald S., Rauch A., Neuber S., Bergmann C., Günzel D, & Halbritter J. (2021). Defective claudin-10 causes a novel variation of HELIX syndrome through compromised tight junction strand assembly. Genes & Diseases, 9(5), 1301-1314.

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Structural Analysis of Cadherin Proteins

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Structures of cadherin proteins containing at least two EC repeats were collected from the Protein Data Bank (Table S1). EC N was aligned to EC N+1 for each pair and Singular Value Decomposition was used to calculate the principal components of the EC N repeat and the original and aligned positions. The angles between the respective components were calculated to determine the tilt (between the first components) and azimuthal (average of the second and third components) angles. Models were constructed in PyMOL (Schrodinger) and then Modeller (Šali and Blundell, 1993 (link)) was used to generate the EC1-6 homology model.

Nicoludis J.M., Lau S.Y., Schärfe C.P., Marks D.S., Weihofen W.A, & Gaudet R. (2015). Structure and sequence analyses of clustered protocadherin reveal antiparallel interactions that mediate homophilic specificity. Structure (London, England : 1993), 23(11), 2087-2098.

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Structural Analysis of UCH37 and its Complexes

Cited 2 times

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Molecular models were generated using Modeller[59 (link)] and MacroModel (Schrodinger, New York, NY). PfUCH37 was modelled using an ensemble of available UCH37 X-ray crystal structures (PDB IDs: 3A7S and 3IHR, 44% and 36% sequence identity respectively), including the complex of TsUCH37 with ubiquitin (37% sequence identity; PDB ID: 4IG7). The structures of PfUCH37 and TsUCH37 (PDB ID: 4IG7) were minimized using the MMF94s forcefield in Sybyl-X 2.1.1 (Certara L.P., St Louis, MO), with the final structure having more than 95% of residues in the allowed region of a Ramachandran plot. Ubiquitin and Nedd8 were docked into the structures of UCH37 using Piper (Schrodinger, New York, NY), with the available X-ray crystal structure of TsUCH37 in complex with ubiquitin (PDB ID: 4IG7) used to guide protein docking. The models of the complexes were minimised using the MMF94s forcefield in Sybyl-X 2.1.1 as described above. The quality of all the models were confirmed with Verify3D[60 (link)]. The structural consequences of the differences in interfacial residues were analysed to assess the structural importance of the residues[41 (link),61 (link)–63 (link)]. Interactions were calculated using Arpeggio[64 (link)] and model structures were examined using Pymol.

Karpiyevich M., Adjalley S., Mol M., Ascher D.B., Mason B., van der Heden van Noort G.J., Laman H., Ovaa H., Lee M.C, & Artavanis-Tsakonas K. (2019). Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathogens, 15(10), e1008086.

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Structural Modeling of FIIa-CP-MPO Hexamer

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In view that mature myeloperoxidase molecule consists of two identical MPO monomers bridged by a disulfide bond we regarded the overall structure of the complex “FIIa-CP-MPO-MPO-CP-FIIa” as a hexamer. Our models for this hexameric structure were proposed on the basis of 3F9P structure (MPO-MPO) (Carpena et al. 2008 ) from the PDB database (http://rcsb.org) and published structures (Samygina et al. 2013 (link); Sokolov et al. 2015b (link)) using PyMOL (Schrödinger LLC 2020), MODELLER (Eswar et al. 2008 ), and GROMACS (Abraham et al. 2015 (link)) software. Glycosylation was constructed using the Glycamgmml software toolkit. Docking was performed using hdocklite, while only FIIa were considered as mobile molecules. Further, from all possible FIIa positions, only those that are sterically compatible with the glycosylation of CP-MPO were selected; it was also assumed that the binding sites of both FIIa molecules are symmetric in the heterohexamer structure. The resulting structures were used for the theoretical calculation of SANS spectra. Theoretical SANS spectra were calculated using the CRYSON programs from the ATSAS package (Franke et al. 2017 (link)).

Zabrodskaya Y.A., Egorov V.V., Sokolov A.V., Shvetsov A.V., Gorshkova Y.E., Ivankov O.I., Kostevich V.A., Gorbunov N.P., Ramsay E.S., Fedorova N.D., Bondarenko A.B, & Vasilyev V.B. (2022). Caught red handed: modeling and confirmation of the myeloperoxidase ceruloplasmin alpha-thrombin complex. Biometals, 35(6), 1157-1168.

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