The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

ABSTRACT: We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We eval

SUBMITTER: Lee W 

PROVIDER: S-EPMC4921114 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature