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BeEP Server: using evolutionary information for quality assessment of protein structure models

BeEP Server: using evolutionary information for quality assessment of protein structure models
BeEP Server: using evolutionary information for quality assessment of protein structure models
The BeEP Server is an online resource aimed to help in the endgame of protein structure prediction. It is able to rank submitted structural models of a protein through an explicit use of evolutionary information, a criterion differing from structural or energetic considerations commonly used in other assessment programs. The idea behind BeEP (Best Evolutionary Pattern) is to benefit from the substitution pattern derived from structural constraints present in a set of homologous proteins adopting a given protein conformation. The BeEP method uses a model of protein evolution that takes into account the structure of a protein to build site-specific substitution matrices. The suitability of these substitution matrices is assessed through maximum likelihood calculations from which position-specific and global scores can be derived. These scores estimate how well the structural constraints derived from each structural model are represented in a sequence alignment of homologous proteins. Our assessment on a subset of proteins from the Critical Assessment of techniques for protein Structure Prediction (CASP) experiment has shown that BeEP is capable of discriminating the models and selecting one or more native-like structures. Moreover, BeEP is not explicitly parameterized to find structural similarities between models and given targets, potentially helping to explore the conformational ensemble of the native state.
0305-1048
Palopoli, N.
d1f4e3af-1a6e-4faf-9257-7c6f169edda9
Lanzarotti, E.
e395be47-4aba-4929-9d84-b7ecde25f774
Parisi, G.
7208c501-7039-490c-8305-db84a5864964
Palopoli, N.
d1f4e3af-1a6e-4faf-9257-7c6f169edda9
Lanzarotti, E.
e395be47-4aba-4929-9d84-b7ecde25f774
Parisi, G.
7208c501-7039-490c-8305-db84a5864964

Palopoli, N., Lanzarotti, E. and Parisi, G. (2013) BeEP Server: using evolutionary information for quality assessment of protein structure models. Nucleic Acids Research. (doi:10.1093/nar/gkt453).

Record type: Article

Abstract

The BeEP Server is an online resource aimed to help in the endgame of protein structure prediction. It is able to rank submitted structural models of a protein through an explicit use of evolutionary information, a criterion differing from structural or energetic considerations commonly used in other assessment programs. The idea behind BeEP (Best Evolutionary Pattern) is to benefit from the substitution pattern derived from structural constraints present in a set of homologous proteins adopting a given protein conformation. The BeEP method uses a model of protein evolution that takes into account the structure of a protein to build site-specific substitution matrices. The suitability of these substitution matrices is assessed through maximum likelihood calculations from which position-specific and global scores can be derived. These scores estimate how well the structural constraints derived from each structural model are represented in a sequence alignment of homologous proteins. Our assessment on a subset of proteins from the Critical Assessment of techniques for protein Structure Prediction (CASP) experiment has shown that BeEP is capable of discriminating the models and selecting one or more native-like structures. Moreover, BeEP is not explicitly parameterized to find structural similarities between models and given targets, potentially helping to explore the conformational ensemble of the native state.

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More information

Published date: 31 May 2013
Organisations: Centre for Biological Sciences

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Local EPrints ID: 353561
URI: http://eprints.soton.ac.uk/id/eprint/353561
ISSN: 0305-1048
PURE UUID: 1b9c0650-4e7a-4dc9-a7e9-8fe2b1f92309

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Date deposited: 10 Jun 2013 13:21
Last modified: 14 Mar 2024 14:07

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Contributors

Author: N. Palopoli
Author: E. Lanzarotti
Author: G. Parisi

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