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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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Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.

(2010) BMC Struct Biol 10

PubMed: 20961427 | PubMedCentral: PMC2974730 | DOI: 10.1186/1472-6807-10-36

Table 3 Evaluation of the success rate (ACC) of predicting IFR ensemble PDB ID Subfamily Organism TP TN FP FN ACC 1FY8 Trypsin Bos taurus 44 244 0 0 1 3TGI Trypsin Bos taurus 42 239 5 0 0.98 1TPA Tryp... in Bos taurus 44 240 1 3 0.98 3BTK Trypsin Bos taurus 43 241 1 4 0.98 3TPI Trypsin Bos taurus 43 242 1 2 0.98 2PTC Trypsin Bos taurus 44 241 0 3 0.98 2TGP Trypsin Bos taurus 45 240 0 3 0.98 4TPI Trypsin Bos taurus 44 239 1 4 0.98 2TPI Trypsin Bos taurus 44 241 1 2 0.98 1BZX Trypsin Bos taurus 43 242 2 1 0.98 1BRB Trypsin Rattus novergicus 41 236 2 2 0.98 1FAK Coagulation factor VIII Homo sapiens 44 247 6 0 0.97 1CBW Chymotrypsin Bos taurus 44 238 5 1 0.97 1MTN Chymotrypsin Bos taurus 45 239 1 3 0.98 2KAI Kallikrein Bos taurus 57 224 0 4 0.98 1EAW Matriptase MTSP1 Homo sapiens 42 241 4 1 0.98 The true positives (TP) are IFR residues present in both the native and the rigid body docked complexes.

Publication Year: 2010


How structure defines affinity in protein-protein interactions.

(2014) PLoS One 9

PubMed: 25329579 | PubMedCentral: PMC4199723 | DOI: 10.1371/journal.pone.0110085

In addition, we excluded a complex where an N-terminal tail close to the binding interface is missing from the structure but is strongly influencing the affinity measurements (PDB ID:2TGP), a complex ... here two different interfaces are too close to each other to analyze them independently (PDB ID:1NVU), and a complex that has been reported to exhibit an exceptionally high level of disorder-to-order transition [26] (PDB ID:2OZA).

In addition, we excluded a complex where an N-terminal tail close to the binding interface is missing from the structure but is strongly influencing the affinity measurements (PDB ID:2TGP), a complex where two different interfaces are too close to each other to analyze them independently (PDB ID:1NVU), and a complex that has been reported to exhibit an exceptionally high level of disorder-to-order transition [26] (PDB ID:2OZA).

Publication Year: 2014