A Grid-enabled web portal for NMR structure refinement with AMBER | Zendy

Ivano Bertini | Zendy; David A. Case | Zendy; Lucio Ferella | Zendy; Andrea Giachetti | Zendy; Antonio Rosato | Zendy

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A Grid-enabled web portal for NMR structure refinement with AMBER

Author(s) -

Ivano Bertini,

David A. Case,

Lucio Ferella,

Andrea Giachetti,

Antonio Rosato

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr415

Subject(s) - computer science , conformational isomerism , force field (fiction) , molecular dynamics , computational science , chemistry , computational chemistry , molecule , artificial intelligence , organic chemistry

The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20-40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols.

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