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Side-chains:
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NOEs:
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Structure from NMR restraints:
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GeNMR
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CS23D
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Torsion angles from chemical shifts:
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Secondary structure from chemical shifts:
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Flexibility from chemical shifts:
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Chemical shifts re-referencing:
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RPF scores
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NMR spectrum prediction:
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Flexibility from structure:
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Methyl S2
B-factor
Molecular dynamics:
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From structure:
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Sparta+
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CH3shift- Methyl
ArShift- Aromatic
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Proshift
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From sequence:
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Camcoil
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Disordered proteins:
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Format conversion & validation:
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From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
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Protein solubility:
camLILA
ccSOL
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Default The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

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 evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25Â*kDa that had 27â??98Â*% sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.



Source: Journal of Biomolecular NMR
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