MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

Advances in structural genomics and protein structure prediction require the design of automatic, fast, objective, and well benchmarked methods capable of comparing and assessing the similarity of low‐resolution three‐dimensional structures, via experimental or theoretical approaches. Here, a new me...

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Bibliographic Details
Published in:Protein science 2002-11, Vol.11 (11), p.2606-2621
Main Authors: Ortiz, Angel R., Strauss, Charlie E.M., Olmea, Osvaldo
Format: Article
Language:English
Subjects:
Algorithms
Computer Simulation
Databases, Protein
Humans
model evaluation
Models, Molecular
Protein Conformation
Protein Folding
Protein structural alignment
protein structure prediction
Protein Structure, Secondary
Proteins - chemistry
Software
Statistics as Topic
structural genomics
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Summary:Advances in structural genomics and protein structure prediction require the design of automatic, fast, objective, and well benchmarked methods capable of comparing and assessing the similarity of low‐resolution three‐dimensional structures, via experimental or theoretical approaches. Here, a new method for sequence‐independent structural alignment is presented that allows comparison of an experimental protein structure with an arbitrary low‐resolution protein tertiary model. The heuristic algorithm is given and then used to show that it can describe random structural alignments of proteins with different folds with good accuracy by an extreme value distribution. From this observation, a structural similarity score between two proteins or two different conformations of the same protein is derived from the likelihood of obtaining a given structural alignment by chance. The performance of the derived score is then compared with well established, consensus manual‐based scores and data sets. We found that the new approach correlates better than other tools with the gold standard provided by a human evaluator. Timings indicate that the algorithm is fast enough for routine use with large databases of protein models. Overall, our results indicate that the new program (MAMMOTH) will be a good tool for protein structure comparisons in structural genomics applications. MAMMOTH is available from our web site at http://physbio.mssm.edu/∼ortizg/.
ISSN:0961-8368
1469-896X
DOI:10.1110/ps.0215902