Abstract
One of the main reasons why ab initio protein structure predictors do not perform very well is their inability to reliably identify long-range interactions between amino acids. To achieve reliable long-range interactions, all potential pairings of beta-strands (beta-topologies) of a given protein are enumerated. The beta-topologies are enumerated such that it is certain that the native beta-topology is among the enumerated. [full abstract] Two very different beta-topology scoring methods from the literature are used to rank potential beta-topologies. This has not previously been attempted for any scoring method. The main result of this paper is that in particular one of the scoring methods consistently top-ranks native beta-topologies.
Since the number of potential beta-topologies grows exponentially with the number of beta-strands, it is unrealistic to expect that all potential beta-topologies can be enumerated and scored for large proteins. The second result of this paper is an enumeration scheme of a subset of beta-topologies. It is shown that native-consistent beta-topologies often are among the top-ranked beta-topologies of this subset.
The presence of the native or native-consistent beta-topologies in the subset of enumerated potential beta-topologies relies heavily on the correct identification of strands. The third contribution of this paper is a method to deal with the inaccuracies of secondary structure predictors when enumerating potential beta-topologies.
The results reported in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. They indicate that decoy generation can be constrained using top-ranked beta-topologies as they are very likely to contain native or native-consistent beta-topologies.
Since the number of potential beta-topologies grows exponentially with the number of beta-strands, it is unrealistic to expect that all potential beta-topologies can be enumerated and scored for large proteins. The second result of this paper is an enumeration scheme of a subset of beta-topologies. It is shown that native-consistent beta-topologies often are among the top-ranked beta-topologies of this subset.
The presence of the native or native-consistent beta-topologies in the subset of enumerated potential beta-topologies relies heavily on the correct identification of strands. The third contribution of this paper is a method to deal with the inaccuracies of secondary structure predictors when enumerating potential beta-topologies.
The results reported in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. They indicate that decoy generation can be constrained using top-ranked beta-topologies as they are very likely to contain native or native-consistent beta-topologies.
| Originalsprog | Engelsk |
|---|---|
| Titel | Proceedings of the World Congress on Engineering and Computer Science 2010 |
| Redaktører | S. I. Ao, Craig Douglas, W. S. Grundfest, Jon Burgstone |
| Antal sider | 5 |
| Vol/bind | 2 |
| Forlag | Newswood Limited |
| Publikationsdato | 2010 |
| Sider | 624-628 |
| ISBN (Trykt) | 978-988-18210-0-3 |
| Status | Udgivet - 2010 |
| Begivenhed | World Congress on Engineering and Computer Science 2010 (WCECS) - San Francisco, USA Varighed: 20 okt. 2010 → 22 okt. 2010 |
Konference
| Konference | World Congress on Engineering and Computer Science 2010 (WCECS) |
|---|---|
| Land/Område | USA |
| By | San Francisco |
| Periode | 20/10/2010 → 22/10/2010 |
Emneord
- Det Natur- og Biovidenskabelige Fakultet
- protein
- bioinformatik