ArticleProtein science : a publication of the Protein Society2018
Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics.Journal of structural biology: X · 2023Article
- Forging tools for refining predicted protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
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4 authors.
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Abstract
This paper reports a method for high-accuracy protein structural refinement, which is a direct extension of the method in our recent publication (Zang, J Chem Phys 2018; 149:072319). It combines a parallel continuous simulated tempering (PCST) method with a temperature-dependent restraint and a blind model selection scheme. In this work, a single-reference-based restraint in previous work was changed to an ensemble-based model (EBM), in which the non-bonded Lennard-Jones term for each contacting atomic pair in previous restraining potential was replaced by a multi-Gaussian function whose parameters are derived from an ensemble of structures such as the ones from various CASP participating groups. The purpose of EBM is to take advantage of partial "correctness" distributed among members of the structural ensemble. Totally 18 targets were refined from the refinement category of CASP10, CASP11 and CASP12. In Top-1 group, 11 out of 18 targets had better models (greater GDT_TS scores) than the CASPR participants. In Top-5 group, nine out of 18 were better. Our results show that PCST-EBM method can considerably improve the low-accuracy structures.
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