Applying Undertaker to quality assessment

Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM‐T08‐MQAO), a function which added other single‐model terms to the distance constraints (SAM‐T08‐MQAU), and a function which used both single‐model and consensus terms (SAM‐T08‐MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT_TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing trustworthiness estimates for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single‐model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments. Proteins 2009. © 2009 Wiley‐Liss, Inc.

[1]  Anna Tramontano,et al.  Assessment of predictions in the model quality assessment category , 2007, Proteins.

[2]  Jonathan Casper,et al.  Combining local‐structure, fold‐recognition, and new fold methods for protein structure prediction , 2003, Proteins.

[3]  K Fidelis,et al.  A large‐scale experiment to assess protein structure prediction methods , 1995, Proteins.

[4]  Kevin Karplus,et al.  Model quality assessment using distance constraints from alignments , 2009, Proteins.

[5]  Liam J. McGuffin,et al.  Benchmarking consensus model quality assessment for protein fold recognition , 2007, BMC Bioinformatics.

[6]  David Baker,et al.  Ranking predicted protein structures with support vector regression , 2007, Proteins.

[7]  Qing Zhang,et al.  The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema , 2004, Nucleic Acids Res..

[8]  Jeffrey Skolnick,et al.  Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential , 2008, Proteins.

[9]  Adrian A Canutescu,et al.  Access the most recent version at doi: 10.1110/ps.03154503 References , 2003 .

[10]  Arne Elofsson,et al.  Prediction of global and local model quality in CASP7 using Pcons and ProQ , 2007, Proteins.

[11]  Yang Zhang,et al.  Template‐based modeling and free modeling by I‐TASSER in CASP7 , 2007, Proteins.

[12]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[13]  Kevin Karplus,et al.  Applying undertaker cost functions to model quality assessment , 2009, Proteins.