Analysis of free modeling predictions by RBO aleph in CASP11.
The CASP experiment is a biannual benchmark for assessing protein structure prediction methods. In CASP11, RBO Aleph ranked as one of the top-performing automated servers in the free modeling category. This category consists of targets for which structural templates are not easily retrievable. We analyze the performance of RBO Aleph and show that its success in CASP was a result of its ab initio structure prediction protocol. A detailed analysis of this protocol demonstrates that two components unique to our method greatly contributed to prediction quality: residue-residue contact prediction by EPC-map and contact-guided conformational space search by model-based search (MBS). Interestingly, our analysis also points to a possible fundamental problem in evaluating the performance of protein structure prediction methods: Improvements in components of the method do not necessarily lead to improvements of the entire method. This points to the fact that these components interact in ways that are poorly understood. This problem, if indeed true, represents a significant obstacle to community-wide progress. Proteins 2016; 84(Suppl 1):87-104. © 2015 Wiley Periodicals, Inc.
Department of Electrical Engineering and Computer Science, Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Mahmoud
M
Mabrouk
Department of Electrical Engineering and Computer Science, Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Tim
T
Werner
Department of Electrical Engineering and Computer Science, Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Michael
M
Schneider
Department of Electrical Engineering and Computer Science, Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany.
Ines
I
Putz
Department of Electrical Engineering and Computer Science, Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, 10587, Germany. oliver.brock@tu-berlin.de.
Oliver
O
Brock
D000465:Algorithms; D001419:Bacteria / Q000737:chemistry; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D007391:International Cooperation; D020407:Internet; D008958:Models, Molecular; D015233:Models, Statistical; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins
CASP; ab initio structure prediction; conformational space search; contact prediction; free modeling; structure prediction pipeline