Phyre

[…] The full-length BtCalV/A10, GII.4.1997.Lordsdale HuNoV, GI.1 human sapovirus, GV.1 MNV, and BtNoV capsid sequences () were submitted to the Protein Homology/analogy Recognition Engine V2.0 (PHYRE2) server () and analyzed using Intensive Mode. Homology modeling of the BtCalV/A10 and BtNoV sequences was based on the known HuNoV GII.4/VA387 (PDB ID: 2OBT) () and HuNoV GII.4.2012/NSW0514 bou […]

[…] vels of ociad1 and ociad2. For predicting structure of zebrafish, mouse, and human OCIAD1 and OCIAD2 proteins, various structure prediction programs such as RaptorX (http://raptorx.uchicago.edu/) and Phyre (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) were used wherein the amino acid sequences of these proteins corresponding to Uniprot IDs Q6NYD7, Q9CRD0, Q9NX40, Q5RHX2, Q9D8W7 and Q […]

[…] Given the good quality of our cryo-EM map, unambiguous assignment of YaxA and YaxB was straightforward (see Supplementary Movie ). A full model of YaxB was obtained with the Phyre2 One-to-one threading service based on the complete model of PaxB (chain A). YaxA and YaxB were first placed by rigid body fitting of the monomers into the density map using Coot. Further implem […]

[…] analyses. Multiple orthologous sequence alignment revealed that R111C has been identified in a highly conserved region across different species (Fig. ). We then performed molecular modeling with the Phyre2 server in automated mode. The variant R111C was found to be located in the helix domain, which could serve to increase the number of hydrogen bonds within the surrounding space (Fig. ). These f […]

[…] function [].Besides its presence in GH43 enzymes, β-sandwich domains are also present in β-glucanases, lectins, cellulases, laminarinases, and sialidases, as revealed by a search with the DALI [] and PHYRE [] servers. The highest structural similarity to a non-GH43 enzyme is observed for the hybrid Bacillus (1,3–1,4)-β-glucanase H(A16-M) (PDB 1AYH; DALI Z-score 14.8; RMSD of 3.0 Å for 164 Cα atoms […]

[…] ions in silico at the CCTOP web server (). The signal peptide prediction was also done by submitting the sequences to SignalP 4.1 server (). The homology modeling of transporter 3D structure used the Phyre2 protein homology/analogy recognition engine (), the Modeller (), and UCSF Chimera () programs. The closest AsCRD1 and AsCCC2 homologs among the RCSB Protein Data Bank (PDB) entries used for com […]