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. Author manuscript; available in PMC: 2012 Aug 1.
Published in final edited form as: Proteins. 2011 May 31;79(8):2389–2402. doi: 10.1002/prot.23049

Figure 4.

Figure 4

A) Balance between model completeness and accuracy for different alignment methods. Average completeness and accuracy of Blast and PSI-Blast algorithms with standard parameters are represented as blue and green circles, respectively, while FFAS results are shown as a curve representing a wide range of ‘base level’ values used in the dynamic programming algorithm (‘base level’ values are shown as labels below the curve describing FFAS results). The results were obtained using a comprehensive Benchmark for alignment accuracy (see Methods section for more details). B) The percentage of models from the alignment accuracy benchmark fulfilling different criteria of completeness and accuracy depending as a function of the ‘base level’ parameter of FFAS (see Methods). Green curve shows the percentage of models with completeness higher than 60% and CαRMSD to the real structure below 3.0Å, blue - models with completeness > 60% and CαRMSD < 2.0Å, orange - models with completeness > 80% and CαRMSD < 3.0Å, and red - models with completeness > 80% and CαRMSD < 2.0Å.