Sentence examples for pdb I from inspiring English sources

The second example is compounds extracted from the Protein Data Bank (PDB) i.e. where C-P becomes an "is-a-ligand-of" relationship.

A conformer is added to the rotamer library of a fragment if it is seen at least four times in the structure databases (combined CSD and PDB), i.e. it can be considered a likely conformation for that fragment.

Moreover, obtaining a homology model for this kinase domain is not trivial because the more similar protein in the PDB (i.e., the catalytic domain of human ZIP kinase; PDB code 1YRP) has a pairwise sequence alignment with hIKK-2 of only 217 residues long, with a low percentage of sequence identity (i.e., 32%).

The sequence and profile are then compared against all sequences in the PDB (i.e., the pdbaa database [29]), and the top hits are ranked by sequence identity (i.e., the number of exactly matched residues in the alignment divided by the length of the query sequence).

In the major sections that follow in this article, we address several areas of quality assurance at the RCSB PDB: (i) hardware redundancy and failover; (ii) weekly database updates; (iii) software releases; (iv) monitoring and troubleshooting tools and practices.

Next, we filtered all chains in the NCDB set against the CDB set and the chains in the PDB, i.e. we remove a given chain from the NCDB set in case if this sequence occurs in the CDB set or in the PDB.

The study identified three potential inhibitors having PDB Id 19V, 6Q8 and 39H.

In silico docking studies on Human topoisomerase IIbeta (PDB Id: 3QX3) have been performed for all molecules (KM10 17) synthesized.

Three-dimensional coordinates of β-CD (PDB Id: 1DMB) were sourced from http://www.rcsb.org/ while FLN was sourced from the UCSF ZINC database (ZINC19360739) [54].

The structure of S. typhi Ty21a OmpF (PDB Id: 3NSG) determined at 2.8 Å resolution by X-ray crystallography shows a 16-stranded β-barrel with three β-barrel monomers associated to form a trimer.

A series of (R -2-(4′-chloR -2-nyl)-3-(4′-chlorophenyl -3-,3,5-tetrahydrobenzo[4′-chlorophenyl -3-pyrimidin-4′-chlorophenyl -3-re designed and docked on the FtsZ protein crystal structure (PDB Id: 1RLU, resolution 2.08 Å).