The emerging role of physical modeling in the future of structure determination
- PMID: 29554555
- DOI: 10.1016/j.sbi.2018.03.005
The emerging role of physical modeling in the future of structure determination
Abstract
Biomolecular structure determination has long relied on heuristics based on physical insight; however, recent efforts to model conformational ensembles and to make sense of sparse, ambiguous, and noisy data have revealed the value of detailed, quantitative physical models in structure determination. We review these two key challenges, describe different approaches to physical modeling in structure determination, and illustrate several successes and emerging technologies enabled by physical modeling.
Copyright © 2018 Elsevier Ltd. All rights reserved.
Similar articles
-
Modeling robust QSAR.J Chem Inf Model. 2006 Nov-Dec;46(6):2310-8. doi: 10.1021/ci050314b. J Chem Inf Model. 2006. PMID: 17125174
-
Bayesian inference of conformational state populations from computational models and sparse experimental observables.J Comput Chem. 2014 Nov 15;35(30):2215-24. doi: 10.1002/jcc.23738. Epub 2014 Sep 24. J Comput Chem. 2014. PMID: 25250719
-
Contact-assisted protein structure modeling by global optimization in CASP11.Proteins. 2016 Sep;84 Suppl 1:189-99. doi: 10.1002/prot.24975. Epub 2016 Jan 11. Proteins. 2016. PMID: 26677100
-
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.Annu Rev Biophys Biomol Struct. 2006;35:115-33. doi: 10.1146/annurev.biophys.35.040405.102010. Annu Rev Biophys Biomol Struct. 2006. PMID: 16689630 Review.
-
Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods.Biochim Biophys Acta Proteins Proteom. 2017 Nov;1865(11 Pt B):1654-1663. doi: 10.1016/j.bbapap.2017.06.016. Epub 2017 Jun 22. Biochim Biophys Acta Proteins Proteom. 2017. PMID: 28648524 Review.
Cited by
-
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins.Methods. 2021 Sep;193:116-135. doi: 10.1016/j.ymeth.2021.03.018. Epub 2021 Apr 6. Methods. 2021. PMID: 33831596 Free PMC article.
-
MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.J Chem Inf Model. 2025 Feb 24;65(4):1685-1693. doi: 10.1021/acs.jcim.4c02108. Epub 2025 Feb 2. J Chem Inf Model. 2025. PMID: 39893583 Review.
-
An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling.Front Mol Biosci. 2021 Aug 12;8:676268. doi: 10.3389/fmolb.2021.676268. eCollection 2021. Front Mol Biosci. 2021. PMID: 34476238 Free PMC article.
-
Computational methods for exploring protein conformations.Biochem Soc Trans. 2020 Aug 28;48(4):1707-1724. doi: 10.1042/BST20200193. Biochem Soc Trans. 2020. PMID: 32756904 Free PMC article. Review.
-
Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era.Brief Bioinform. 2025 Jul 2;26(4):bbaf340. doi: 10.1093/bib/bbaf340. Brief Bioinform. 2025. PMID: 40663654 Free PMC article. Review.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources