SWISS-MODEL

[…] (http://disulfind.dsi.unifi.it/) was used to predict cysteine disulfide bonding state and connectivity of the putative protein. and the tertiary structure of bdpho was predicted by online software swiss-model (https://swissmodel.expasy.org/) (biasini et al. )., the phylogenetic analysis on the basis of amino acid sequences was performed with mega 6.0 (tamura et al. ) using the maximum […]

[…] the isoelectric point (pi) and molecular weight (mw) of the mature proteins were calculated with the expasy online tool compute pi/mw., three-dimensional structures of proteins were modeled with the swiss-model server, selecting nine gene models in the protein structure model database to build the models []. the sequence identity values between the template (rnase1) and the nine studied genes […]

[…] also used to analyze the pgds enzyme with assemblies of different conformers., the 2d secondary structure prediction of pgds was performed using psipred server [], and the 3d model was generated by swiss-model[]. the structure validation and quality control was done by procheck [] and whatcheck module on whatif server []., pgds activity was assayed using γ-pga as the substrate. γ-pga […]

[…] the brillianstar-lt assay system (toyo-b-net) and the 2030 arvo x multilabel counter instrument (perkinelmer) according to the manufacturers’ procedures., homology modeling was performed using the swiss-model server [–]. after blast searches [] of the bobcat and puma a3z3 amino acid sequences against protein data bank sequence entries (http://www.rcsb.org/pdb/), the crystal structure of human […]

[…] parasite enzymes was identified using clustal omega (https://www.ebi.ac.uk/tools/msa/clustalo/). template for structural modeling was identified using pdb-blast. protein model was developed using swiss-model (https://swissmodel.expasy.org/) [–] and verified with ramachandran plot, procheck analysis, global model quality estimation (gmqe) score and qualitative model energy analysis (qmean) […]

[…] amino acids were removed for further analysis. meme (version 4.12.0) was used to search for conserved motifs, and the number of motifs was set as 10 []. the protein structure was predicted using the swiss-model database []. the interaction networks of a. thaliana bes1 genes were constructed using the string database (http://string-db.org). the rna-seq data was used to analyse bes1 gene […]

[…] ha structures of the other representatives from homology modelling described in the next section. avian and human receptor analogs were obtained from pdb:5e2z [] and 2yp3 [] respectively., we used swiss-model for the homology modelling, constructing an atomic-resolution model of the target ha protein from its amino acid sequence [, ]. first, the primary sequence of the ha protein from the tw17 […]

[…] (https://www.ncbi.nlm.nih.gov/tools/cobalt/). the predictprotein was used to perform go terms, protein-protein and protein-dna binding sites and sub-cellular localization (yachdav et al., ). the swiss-model was used to predict protein tertiary structure (biasini et al., )., genes involved in oil biosynthesis for arabidopsis were obtained from the arabidopsis lipid gene database (mekhedov) […]

[…] experiments is shown., the three-dimensional (3d) model of haqp8 was generated using as template the crystallographic structure of haqp5 (3d9s; resolution = 2 å) (). the tetramer was built using swiss-model web server () and validated through the prosa web interface (), where the global quality of each chain was assessed through the z score (−5.73, −5.62, −5.69, and −5.58) (fig. s5b). […]

[…] signal peptides were predicted using the signalp 4.1 server (). the molecular weights of the proteins were predicted using swiss-prot. three-dimensional models of ehippbp1 were predicted using the swiss model online tools (). template search with blast () and hhblits () in default parameters has been performed against the swiss-model template library (smtl, last update: 2017-12-06, last […]