Extended Sampling of Macromolecular Conformations from Uniformly Distributed Points on Multidimensional Normal Mode Hyperspheres
Antoniel A. S. Gomes, Mauricio G. S. Costa, Maxime Louet, Nicolas Floquet, Paulo M. Bisch, David Perahia · 2024
Read Extended Sampling of Macromolecular Conformations from Uniformly Distributed Points on Multidimensional Normal Mode Hyperspheres by Antoniel A. S. Gomes, Mauricio G. S. Costa, Maxime Louet, Nicolas Floquet, Paulo M. Bisch, David Perahia (2024) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-11672670.txt.
Description
Antoniel Gomes and five co-authors wrote a 2024 paper on a new way to sample the shapes a protein can take. Proteins bend and flex, and their range of shapes decides what they can do. A classic tool, normal mode analysis, describes the main directions of that flexing. Combining those directions well is the hard part.
Their method spreads points evenly over spheres in the space of combined motions. Structures are then built at those even spacings and relaxed with standard molecular dynamics runs. Tests on two proteins, egg-white lysozyme and a human liver enzyme, show the method covers shape space well. Its ensembles matched known experimental structures better as more motions were added. The approach, called dpMDNM, gives modelers a systematic way to explore protein motion.
Catalog record
| CREATOR | Antoniel A. S. Gomes, Mauricio G. S. Costa, Maxime Louet, Nicolas Floquet, Paulo M. Bisch, David Perahia |
|---|---|
| YEAR | 2024 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 62 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |