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F1000Res. 2014 Jan 21;3:17. doi: 10.12688/f1000research.3-17.v1. eCollection 2014.

Ranking the quality of protein structure models using sidechain based network properties.

Author information

1
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India ; I.I.Sc. Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India.
2
I.I.Sc. Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India.

Abstract

Determining the correct structure of a protein given its sequence still remains an arduous task with many researchers working towards this goal. Most structure prediction methodologies result in the generation of a large number of probable candidates with the final challenge being to select the best amongst these. In this work, we have used Protein Structure Networks of native and modeled proteins in combination with Support Vector Machines to estimate the quality of a protein structure model and finally to provide ranks for these models. Model ranking is performed using regression analysis and helps in model selection from a group of many similar and good quality structures. Our results show that structures with a rank greater than 16 exhibit native protein-like properties while those below 10 are non-native like. The tool is also made available as a web-server ( http://vishgraph.mbu.iisc.ernet.in/GraProStr/native_non_native_ranking.html), where, 5 modelled structures can be evaluated at a given time.

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