PMC:1867812 / 49393-51195 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":"5 Conclusions and Ongoing Work\nIn this article, we present a novel approach to analyze protein folding trajectories and a case study on the small proteins BBA5 and GSGS. We capture a variety of structural motifs in the 3D protein conformations by non-local bit-patterns identified in their 2D contact maps. By modeling the interactions or spatial relationships among bit-patterns as SOAPs and SOAP episodes, we effectively characterize the evolutionary nature of the folding process. We also describe two methods to summarize folding trajectories by super-imposing protein specific information and 3D motifs onto SOAPs. Utilizing the summarized trajectories, we demonstrate that one can detect folding events and the temporal order among events. We also show that through comparing such summarized trajectories, one can identify a partial folding pathway common to multiple trajectories.\nWe realize that it is a very hard and challenging task to understand the folding mechanism of proteins. Based on our analysis results over a small protein, we are not in the position to make any general comments on the protein folding problem. However, the approach presented here is general and applicable to any folding trajectories.\nPresently, we are in the process of addressing several other related issues. First, we are automating the mapping between 2D bit-patterns and 3D motifs. Second, we are further analyzing the identified consensus folding pathways and validating them through other means. Third, it is well-known that the side chains of a protein play a crucial role in the folding process. We are currently investigating different approaches to involve side chains in our analysis. Finally, we are investigating whether bit-patterns can be used to index and manage protein folding simulation data.","divisions":[{"label":"title","span":{"begin":0,"end":30}},{"label":"p","span":{"begin":31,"end":887}},{"label":"p","span":{"begin":888,"end":1223}}],"tracks":[]}