Sentence examples for by structural alignments of from inspiring English sources
The sidechains of the monomeric models were minimized for 200 steps and, subsequently, homodimeric models were obtained by structural alignments of the different monomers onto the crystal structure of the C-Jun-homodimer (PDB ID: 1JNM), followed by additional minimization steps.
A comparative view of the binding modes of SB-203580 and BIRB-796 by structural alignment of two X-ray co-crystal structures was utilized to identify this novel series.
The topology based functional residue classification was obtained by structural alignment of identical proteins using Dali facility [20] and subsequent measure of root mean square deviations (RMSD).
Template (b) is mapped to query (a) by structural alignment to form query-template complex (c).
We additionally require that the complete structure is covered by structural alignments; a segment of the query structure longer than 80 residues without any structural matches always disqualifies a strong match.
The cluster trees based on p-distance and LHM were compared using the Phylip program [ 21] by generating 1000 bootstrap alignments from the structural alignments of a protein family and by calculating p-distance based cluster trees from the bootstrap alignments.
Structural alignments of proteins were performed by STAMP [ 29].
In addition, the prediction of protein function remains a serious challenge, but the observation that the active sites of proteins are often the best preserved regions in a divergent family offers a robust method of classifying proteins of unknown function by structural alignment.
Prosup benchmark, prepared by Sippl's group, consists of 127 pairs of proteins with alignment by structural alignment program Prosup [38].
The reference-dependent alignment accuracy is calculated as the percentage of correctly aligned positions judged by reference alignments, which are generated by structural alignment programs.
