AllosMod

[…] tio envelopes were calculated using DAMMIF and also GASBOR, to make use of good data quality in the high angle region. An intitial model of CCP24-25 was obtained by homology modeling using the server ALLOSMOD () and the crystal structure of the CRRY complement receptor (2xrb) as starting template. Two N-glycans were modeled at positions Asn 1534 and Asn 1540 according to the prediction of the NetN […]

[…] glycans (a total of three are bound to the serpinic domain of C1-INH, http://www.uniprot.org/uniprot/P05155) to check for steric clashes. The virtual glycosylation was performed with the help of the Allosmod online server (https://modbase.compbio.ucsf.edu/allosmod/).Molecular graphics were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualizatio […]

[…] ded to the resulting assembled model using the MODELER () “Model/Refine Loops” routine as implemented in Chimera ().Coarse-grained molecular dynamics (MD) simulations were performed using the program Allosmod (). Five independent runs were performed, each consisting of 30 independent trajectories generating 100 models. From this total pool of 15,000 models, automated selection of the minimal set o […]

[…] FN56M binary subcomplex were then extracted from the completed BMP2-eRGMB–NEO1FN56M model. All-atom ensemble modeling of NEO1FN56M, eRGMB, eRGMB–NEO1FN56M and BMP2–eRGMB–NEO1FN56M was performed using AllosMod; and in each case, 50 independent ensembles of 100 models were generated. From this pool, automated selection of the minimal set of models satisfying the scattering data was performed using M […]

[…] further modelling. Missing loops and N- and C termini were added in extended conformations using the program Modeller. All-atom simulations of RPTPσ Ig1-FN3 and sEcto was performed using the program AllosMod. For each starting structure, 30 independent pools of 100 models were generated. For the combined pool, calculation and fitting of scattering patterns was performed using the program FoXS, an […]