Combining physicochemical and evolutionary information for protein contact prediction.

We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein...

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Autores principales:	Michael Schneider, Oliver Brock
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3c4d836df80648e082cc76f0502da619
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spelling	oai:doaj.org-article:3c4d836df80648e082cc76f0502da6192021-11-25T05:55:31ZCombining physicochemical and evolutionary information for protein contact prediction.1932-620310.1371/journal.pone.0108438https://doaj.org/article/3c4d836df80648e082cc76f0502da6192014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0108438https://doaj.org/toc/1932-6203We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information--evolutionary and physicochemical--we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/.Michael SchneiderOliver BrockPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e108438 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michael Schneider Oliver Brock Combining physicochemical and evolutionary information for protein contact prediction.
description	We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information--evolutionary and physicochemical--we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/.
format	article
author	Michael Schneider Oliver Brock
author_facet	Michael Schneider Oliver Brock
author_sort	Michael Schneider
title	Combining physicochemical and evolutionary information for protein contact prediction.
title_short	Combining physicochemical and evolutionary information for protein contact prediction.
title_full	Combining physicochemical and evolutionary information for protein contact prediction.
title_fullStr	Combining physicochemical and evolutionary information for protein contact prediction.
title_full_unstemmed	Combining physicochemical and evolutionary information for protein contact prediction.
title_sort	combining physicochemical and evolutionary information for protein contact prediction.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/3c4d836df80648e082cc76f0502da619
work_keys_str_mv	AT michaelschneider combiningphysicochemicalandevolutionaryinformationforproteincontactprediction AT oliverbrock combiningphysicochemicalandevolutionaryinformationforproteincontactprediction
_version_	1718414392872140800

Combining physicochemical and evolutionary information for protein contact prediction.

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