Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps.

Monika Kurczynska, Ewa Kania, Bogumil M Konopka, Malgorzata Kotulska

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Article in Journal of molecular modeling, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

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2citing papers in PubMed

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2 citing papers in PubMed.

Computer-aided Drug Discovery Approaches in the Identification of Anticancer Drugs from Natural Products: A Review.Current computer-aided drug design · 2025
Review
Automated method to differentiate between native and mirror protein models obtained from contact maps.PloS one · 2018
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4 authors.

Monika KurczynskaFaculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.

Ewa KaniaFaculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.

Bogumil M KonopkaFaculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.

Malgorzata KotulskaFaculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland. malgorzata.kotulska@pwr.edu.pl.

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6 · The paper itself

Abstract

Reconstructing protein structure based on contact maps leads to two types of models: properly oriented models and mirror models. This is due to the fact that contact maps do not include information on protein chirality. Therefore, both types of model orientations share the same contact map and are geometrically allowed. In this work, we verified the hypothesis that some of the energy terms calculated by PyRosetta could be useful to distinguish between properly oriented and mirror models. We studied 440 models of all-alpha protein domains reconstructed manually from their contact maps, where 50% of the models were properly oriented and 50% had mirror orientation. We showed that dihedral angles and energy terms, based on the probability of specific geometrical arrangement of the residues, differed significantly for properly oriented and mirror models.

Indexed as

Models, MolecularProtein DomainsProteinsProtein Structure, SecondaryThermodynamicsProteinsContact mapsEnergy termsMirror imagesProtein structureProtein structure reconstruction

Identifiers

PMID27107578

DOI10.1007/s00894-016-2975-3

PMCPMC4842210

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