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Publication for PROCOGNATE
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
[…] algorithm have already been extensively validated through use of appropriate datasets (PD and PM). Further, in this study a large-scale comparison with the crystallographically derived sites from the Procognate database has been carried out. In 2442 of 3209 complexes, a pocket at a similar location as well as the same ligand association is predicted. The entire site-based function annotation pipel […]
Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests
[…] from the primary literature in the CSA were used.Ligand (substrate, cofactor, intermediate, products and their analogues) information in the Protein Data Bank (PDB) was obtained from the EzCatDB and PROCOGNATE (ver. 1.6) databases. All annotations in the EzCatDB and the cognate ligand entries with similarity scores higher than 0.5 in PROCOGNATE were used. Ligand binding residues were defined fro […]
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions
[…] of the length of the corresponding protein sequence. The dataset contains 803 SASs with 482 disease related and 323 neutral.The presence of cognate ligands in each structure was determined using the Procognate database . The cognate ligands deposited in this database are those involved in the biological function of the proteins. After this filtering we found that 35 proteins have bound/unbound […]
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