Sentence examples for structure based method from inspiring English sources

In order to validate the accuracy of predictions calculated with the Emboss pKa set, a comparison of this set, a more recent pKa set [22], and a structure based method (PDB2PQR/PROPKA [23]) was performed.

The most established approaches [6] for protein function prediction are based on sequence similarity using BLAST [7], sequence motifs such as PROSITE [8], profile methods such as PFAM [9] and PSI-BLAST [7], and structure based method such as FATCAT [10] and ProCAT [10].

As expected, when aligning pairs of proteins with weak sequence homology, a structure based method performs much better.

Structure based methods were used with and without consensus sequence information.

Seven B cell epitopes (B-P1 to B-P7) were predicted by sequence and structure based methods.

In this study we have applied multiple ligand and structure based methods to the PknB problem and then combined these results using data fusion.

In the past, both, ligand and structure based methods intended to predict if a small molecule could cause fatal heart arrhythmias, "torsades de pointe" and sudden death.

However, ligand-based approaches often cover a broader range of binding conformations, but only a small part of possible binding site space at the protein, which is a reason to prefer structure based methods.

Such methods, similar to the more common structure based methods [57, 58], generally do not allow precise (e.g. binding constant error <10-fold) prediction of binding properties of individual compound-target interactions, but they do provide guidance to focus efforts on compound classes or libraries with the best chances for success [59 64].

We found shape based similarity search methods (ROCS and EON) performed significantly better than structure based methods.

We employed domain sequence and structure based methods to infer a model for the evolutionary history of the MAGUKs.