Phyre

[…] 1go9) containing a d-phe residue at position 12 and alpha-aminoisobutyric acid in position 15 ()., for crf-bp, top scoring models produced by threading-based approaches identified by muster and phyre2 servers (, ) were retrieved, aligned, and used as starting templates to generate a human crf-bp model. fragments from gastric intrinsic factor receptor cubilin (pdb: 3kq4) () and neuropilin […]

[…] by the ncbi blast service program. sequence alignments were generated using the clustalw2 program (blackshields et al., )., ehvps2, ehvps20, and ehvps24 amino acid sequences were submitted to the phyre2 server (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) to obtain the proteins 3d predicted structures. results obtained were documented and analyzed through the ucsf chimera […]

[…] the corresponding pul. based on these criteria, fjoacxe (puldb id: fjoh_3879; genbank id: abq06890.1) was selected for recombinant protein expression. a structural model of fjoacxe was built using phyre2.0 [] for the cbm-like domain, using pdb 2o14 as template, and modeller 9.19 [] for the ce/catalytic domain using pdb 2o14 and pdb 1k7c []. the model was displayed with pymolv1.7.4.5 edu (pymol […]

[…] we analyzed the protein structure of the region comprising the end of the i domain through the c domain of the three thalictrum ap3 proteins using protein homology/analogy recognition engine v 2.0 (phyre2; )., to investigate the function of three b-class gene orthologs of the ranunculid t. thalictroides, we conducted targeted vigs using single gene constructs, analyzed gene expression […]

[…] the exon/intron structures of the cadirs were searched and presented as described by kang et al.. prediction of the tertiary structures and homologs of cadirs was conducted through the online server phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id = index) as described by li et al.., information about the chromosomal location of cadirs was obtained from the pepper genome platform […]

[…] structurally compare to known human and animal norovirus capsids, we utilized predictive structural modeling to illustrate the full-length btcalv/a10 and btnov capsid structures. first, we used phyre2 open source software to determine if btcalv/a10 contained known calicivirus capsid structures followed by structural homology modeling using modeller software from the max planck institute […]

[…] well-conserved region (exon 4 to exon 5) within the ocia domain (fig. ). interestingly, in silico analysis using various structure prediction programs such as raptorx (raptorx.uchicago.edu/) and phyre (http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index) showed that the region ranging from exon 3 to exon 6 is indeed an important part of the ociad1/2 genes as it codes for a double […]

[…] with migaslllgav (www.giardiadb.org). cp14019 shows 80% identity to cp16779 and 50% identity to cp10217 and cp16160. the structures of the pro- and mature proteases were predicted using itasser and phyre2 and the structural models aligned well with known cathepsin b structures (fig. s1 to s3, table s3 to s5). cp10217, cp14019 and cp16779 are most similar to trypanosoma congolese procathepsin […]

[…] of 6.6 å (fsc = 0.5)., 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. […]

[…] (, fig. ). a topological model of the ipo13 polypeptide was predicted using smart (http://smart.embl-heidelberg.de/). the crystal structures of wild-type and mutant proteins were predicted using phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and visualized with the pymol software (version 1.5)., total rna was extracted from murine (c57bl/6 strain) tissues, including […]