Sentence examples for using the protein structure from inspiring English sources

The structural quality assessment of the final models was performed using the Protein Structure Validation Suite, as described above.

Second, we identify putative protein targets for each drug using the protein structure database and in-silico virtual docking.

A. Human GBP5 modeled using the protein structure of human GBP1 in the SWISS_MODEL protein homology modeler.

Homology modeling was carried out using the protein structure homology-modeling server SWISS-MODEL (Arnold et al., 2006; Schwede et al., 2003) (http://swissmodel.expasy.org/).org/

Using the protein structure prediction programs PSORT (Nakai and Horton 1999) and SOSUI Hirokawaa et al. 1998), we found silkworm osiris proteins had the same structural features.

The 3D models of the Ups1-Mdm35 and TRIAP1-PRELID1 complexes were constructed using the protein structure threading program PHYRE [ 39] and were refined independently with ModRefiner [ 40].

The output consists of two components: (i) a Jmol applet to visualise and explore the predictions using the protein structures and (ii) a table listing HSPred scores for each interface amino acid.

Other proteins with similar structures were retrieved by the Dali server http://ekhidna.biocenter.helsinki.fi/dali_server/ using the protein structures of the BLAST hits as input.

The structures of the U. gibba orthologs to AXR1, IGS, TAR2, SOL1, DEG9, and DEG10 were modeled using the protein structures with PDB identifiers 2nvuA (2.80 Å) (Huang et al. 2007), 3tsmA (2.15 Å), 3bwnB (2.25 Å) (Tao et al. 2008), 1h8lA (2.60 Å) (Aloy et al. 2001), and 4flnB (2.80 Å) (Sun et al. 2012), respectively, as templates.

We used the protein structure prediction server HHpred (available at http://toolkit.tuebingen.mpg.de/HHpred) to build a homology model of the structure of D. melanogaster Pur-α [15].

Using the protein crystal structure of VEGFR2 and its binding site in the PDB database permitted a resolution of the 3VHE three-dimensional structure at 1.55Å (Fig. 7A).