Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.

Emilia A Lubecka, Cezary Czaplewski, Adam K Sieradzan, Agnieszka G Lipska, Łukasz Dziadek, Adam Liwo

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Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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6 authors.

Emilia A LubeckaFaculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.

Cezary CzaplewskiFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland.

Adam K SieradzanFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland.

Agnieszka G LipskaCentre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland.

Łukasz DziadekFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland.

Adam LiwoFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland. adam.liwo@ug.edu.pl.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Secondary structure is a solid scaffold on which the three-dimensional structure of a protein is built. Therefore, care must be taken to reproduce the secondary structure as accurately as possible in the simulations of protein systems. In this chapter, we summarize the physics-based energy terms that govern secondary-structure formation, the auxiliary restraints on secondary structure derived from bioinformatics and from the experimental data, and the role of those in the modeling of protein structures, dynamics, and thermodynamics with the physics-based coarse-grained UNRES force field. Examples illustrating the methodology discussed and further directions of development are presented.

Indexed as

Molecular Dynamics SimulationProteinsProtein Structure, SecondaryThermodynamicsComputational BiologyModels, MolecularProteinsEnergy functionNMR-based restraintsPhysics-based modelPSIPREDSecondary structureUNRES force fieldVirtual-bond angles

Identifiers

PMID39576573

DOI10.1093/bioinformatics/btaa897

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