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PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Sanjeevini: a freely accessible web-server for target directed lead molecule discovery.

(2012) BMC Bioinformatics 13 Suppl 17

PubMed: 23282245 | PubMedCentral: PMC3521208 | DOI: 10.1186/1471-2105-13-S17-S7

PDBID a Ligand (Molecular formula) EXBFE (kcal/mol)# PBFE (kcal/mol) b PBFE (kcal/mol) c 1 1BRA C 7 H 8 N 2 -2.496 -4.92 -4.59 2 1F0T C 19 H 19 N 5 O 4 S 2 -8.29 -6.92 -7.35 3 1F0U C 27 H 30 N 4 O 3 -... .89 -8.98 -6.96 4 1MTW C 26 H 28 N 4 O 3 -10.076 -7.84 -6.64 5 1PPC C 27 H 31 N 5 O 4 S -8.8 -8.46 -6.85 6 1TNH C 7 H 9 FN -4.59 -4.49 -4.28 7 1TNI C 10 H 15 N -2.32 -3.74 -3.53 8 1TNJ C 8 H 12 N -2.67 -3.72 -3.77 9 1TNK C 9 H 14 N -2.03 -3.81 -3.51 10 1TNL C 9 H 12 N -2.56 -3.56 -3.99 11 1TPP C 10 H 12 N 2 O 3 -7.95 -6.05 -5.55 12 3PTB C 7 H 8 N 2 -6.46 -5.36 -5.27 13 1S0R / 1S0Q C 8 H 10 N 3 O 1 -5.71 -5.25 -5.59 14 1S0R / 1S0Q C8H11N2O1 -6.04 -5.37 -5.51 15 1S0R / 1S0Q C7H10N3 -6.95 -5.16 -5.99 16 1S0R / 1S0Q C7H9N2 -6.35 -5.26 -5.12 17 1S0R / 1S0Q C8H11N2 -6.59 -5.33 -5.56 18 1S0R / 1S0Q C9H13N2 -6.07 -5.01 -5.41 19 1S0R / 1S0Q C10H15N2 -6.14 -5 -5.55 20 1S0R / 1S0Q C 10 H 15 N 2 (iso) -5.42 -5.26 -5.79 21 1S0R / 1S0Q C 11 H 17 N 2 -6.26 -5 -6.08 22 1S0R / 1S0Q C 12 H 19 N 2 -6.5 -5.45 -6.55 23 1S0R / 1S0Q C 13 H 21 N 2 -6.97 -5.82 -6.53 # Experimental binding free energies of trypsin binding molecules.

In addition, some of the known synthetic inhibitors [ 128 ] of bovine pancreatic trypsins, PDBID 1S0R were also docked and scored.

For Bovine pancreatic trypsin receptor, a structure with unknown binding site information (PDBID 1S0Q ) is also available in the literature [ 128 , 129 ] along with a protein-ligand complex (PDBID 1S0R ) which was taken as an input in the first case study.

In the Bovine pancreatic trypsins, the amino acids mainly involved in interactions with the ligand molecules are reported to be Ser 172, Asp 171 and Gly 196 in the target protein (PDBID 1S0R ) [ 104 ].

Publication Year: 2012


Differences in PAR-2 activating potential by king crab (Paralithodes camtschaticus), salmon (Salmo salar), and bovine (Bos taurus) trypsin.

(2013) BMC Res Notes 6

PubMed: 23870109 | PubMedCentral: PMC3733831 | DOI: 10.1186/1756-0500-6-281

a – c : Electrostatic surfaces of (A) king crab trypsin (homology model), (B) bovine trypsin (pdb code: 1s0r), and (C) Atlantic salmon trypsin (pdb code: 1hj8).

The homology model of king crab trypsin, the structures of Atlantic salmon trypsin (pdb code: 1hj8) and bovine trypsin (pdb code: 1s0r) were superimposed on the thrombin-PAR-4 structure (pdb code: 2pv9; [ 26 ]).

Publication Year: 2013