Benchmarking of TASSER in the ab initio limit.

Benchmarking of TASSER in the ab initio limit. Research Abstract Details 

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Benchmarking of TASSER in the ab initio limit. Abstract Text:

Jose M Borreguero,Jeffrey Skolnick,Jose M Borreguero,Jeffrey Skolnick,

A significant number of protein sequences in a given proteome have no obvious evolutionarily related protein in the database of solved protein structures, the PDB. Under these conditions, ab initio or template-free modeling methods are the sole means of predicting protein structure. To assess its expected performance on proteomes, the TASSER structure prediction algorithm is benchmarked in the ab initio limit on a representative set of 1129 nonhomologous sequences ranging from 40 to 200 residues that cover the PDB at 30% sequence identity and which adopt alpha, alpha + beta, and beta secondary structures. For sequences in the 40-100 (100-200) residue range, as assessed by their root mean square deviation from native, RMSD, the best of the top five ranked models of TASSER has a global fold that is significantly close to the native structure for 25% (16%) of the sequences, and with a correct identification of the structure of the protein core for 59% (36%). In the absence of a native structure, the structural similarity among the top five ranked models is a moderately reliable predictor of folding accuracy. If we classify the sequences according to their secondary structure content, then 64% (36%) of alpha, 43% (24%) of alpha + beta, and 20% (12%) of beta sequences in the 40-100 (100-200) residue range have a significant TM-score (TM-score > or = 0.4). TASSER performs best on helical proteins because there are less secondary structural elements to arrange in a helical protein than in a beta protein of equal length, since the average length of a helix is longer than that of a strand. In addition, helical proteins have shorter loops and dangling tails. If we exclude these flexible fragments, then TASSER has similar accuracy for sequences containing the same number of secondary structural elements, irrespective of whether they are helices and/or strands. Thus, it is the effective configurational entropy of the protein that dictates the average likelihood of correctly arranging the secondary structure elements.

Benchmarking of TASSER in the ab initio limit. Publishing Authors By Initials

JM Borreguero,J Skolnick,JM Borreguero,J Skolnick,

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Benchmarking of TASSER in the ab initio limit. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Proteins

VOLUME: 68

Page Numbers: 48-56

Journal Abbreviation: Proteins

ISSN: 1097-0134

DAY: 1

MONTH: Jul

YEAR: 2007

Benchmarking of TASSER in the ab initio limit. Information

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LANGUAGE: eng

NlmUniqueID: 8700181

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Grant and Affiliation Information for Benchmarking of TASSER in the ab initio limit.

AFFILIATION: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM-37408

ACRONYM: GM

MEDLINETA: Proteins

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