PMC:1867812 / 48460-49391 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1867812","sourcedb":"PMC","sourceid":"1867812","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1867812","text":"Currently, we rely on visual tools to justify these consensus pathways. We did attempt to use several measurements that have been used previously to quantify the similarity between 3D protein conformations, but to no avail. These measurements include RMSD, contact order, and native contacts. If we identify the pathway based on the best match given by any of the above measurements, we often ended up with a very short consensus pathway (as short as 10 frames). Two conformations are said to be a best match if they have the lowest RMSD or have the smallest difference in contact order or native contacts. Moreover, different best-matched measurements rendered very different consensus pathways. Finally, we notice that the best-matched conformations based on any of such measurements can often exhibit very different structural characteristics. We are investigating alternative methods for quantitative validation of our results.","tracks":[]}