chemical_shifts Module

The chemical_shifts module provides utilities for predicting NMR chemical shifts from protein structures.

Overview

Chemical shifts are highly sensitive indicators of local secondary structure and environment. This module provides shims to synth-nmr for predicting these values.

Main Functions

::: synth_pdb.chemical_shifts.predict_chemical_shifts options: show_root_heading: true show_source: true

::: synth_pdb.chemical_shifts.calculate_csi options: show_root_heading: true show_source: true

::: synth_pdb.chemical_shifts.get_secondary_structure options: show_root_heading: true show_source: true

Usage Examples

Predicting Chemical Shifts

from synth_pdb.chemical_shifts import predict_chemical_shifts

# structure: biotite.structure.AtomArray
shifts = predict_chemical_shifts(structure)

# shifts: Dict[int, Dict[str, float]]
# {residue_id: {atom_name: shift_value}}

Chemical Shift Index (CSI)

Analyze secondary structure based on H-alpha, C-alpha, and C-beta shifts.

from synth_pdb.chemical_shifts import calculate_csi

csi = calculate_csi(shifts)
# Returns list of -1 (alpha), 1 (beta), 0 (coil)

References

  • Random Coil Shifts: Wishart, D. S., et al. (1995). "1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects." Journal of Biomolecular NMR. DOI: 10.1007/BF00211783
  • Ring Current Effects: Haigh, C. W., & Mallion, R. B. (1979). "Ring current theories in nuclear magnetic resonance." Progress in Nuclear Magnetic Resonance Spectroscopy. DOI: 10.1016/0079-6565(79)80010-2

See Also