Skip to content

Latest commit

 

History

History
134 lines (89 loc) · 4.75 KB

implementation.md

File metadata and controls

134 lines (89 loc) · 4.75 KB
Raw

fingeRNAt implementation details

Detection of interactions

Inspired by PLIP implementation. Applies to SIFt type FULL.

Nucleic acid properties

The nucleic acid's detected properties are as follows:

  • Hydrogen Bonds Acceptors & Donors - detected with OpenBabel
  • Halogen Bonds Acceptors - detected with OpenBabel (same as Hydrogen Bonds Acceptors)
  • Negative charges - assigned to both oxygens (OP1 & OP2) of each residue's phosphate group
  • Aromatic rings - detected with OpenBabel

Ligand properties

The ligand's detected properties are as follows:

  • Hydrogen Bonds Acceptors & Donors - detected with OpenBabel
  • Halogen Bonds Donors - detected with OpenBabel
  • Positive & Negative charges - detected with OpenBabel
  • Aromatic rings - detected with RDKit
  • Lipophilic atoms - detected with RDKit

Molecular Interactions' Geometric Rules

fingeRNAt detects the following nine non-covalent interactions:

1. Hydrogen bonds

Geometric rule:

  • |D - A| < 3.9 Å (Torshin, Weber, & Harrison, 2002)

NOTE: If hydrogens are present in RNA/DNA structure, fingeRNAt can be run with parameter -dha, that additionaly calculates Donor-Hydrogen-Acceptor angle used as supplementary criteria in hydrogen bonds detection:
100° < D-H-A angle < 260° (Adasme et al., 2021)
Parameter -dha applies only to FULL SIFt type, as SIMPLE & PBS do not calculate hydrogen bonds.

2. Halogen bonds

Geometric rules:

  • |X - A| < 4.0 Å (Auffinger et al., 2004)
  • C-X-A angle ~ 165° ± 30° (Auffinger et al., 2004)
  • X-A-A' angle ~ 120° ± 30° (Auffinger et al., 2004)

3. Cation - anion interactions

Geometric rule:

  • 0.5 Å < |cation - anion| < 5.5 Å (Barlow and Thornton, 1983)

NOTE: fingeRNAt considers both oxygens from phosphate group (OP1 and OP2) of RNA/DNA as negatively charged.

4. Pi - cation & 5. Pi - anion interactions

Geometric rules:

  • |cation/anion - aromatic ring center| < 6.0 Å (Gallivan and Dougherty, 1999)
  • angle between the ring plane and the line between cation/anion - ring center ~ 90° ± 30°

NOTE: In case of Pi - cation interaction, aromatic ring is only from the nucleic acid side (as nucleic acids are negatively charged). However, Pi - anion interaction is considered both ways: (i) nucleic acid's aromatic ring - ligands's anion and (ii) nucleic acid's anion (from phosphate group; see above) - ligand's aromatic ring.

6. Pi - stacking interactions

Geometric rules:

  • Common rules for all Pi - stacking interactions' types:

    • |rings' centroids| < 5.5 Å (McGaughey, 1998)
    • rings' outset < 2.0 Å

  • For sandwich & parallel - displaced:

    • angle between the ring planes < 30°

  • For T - shaped:

    • angle between the ring planes ~ 90° ± 30°

NOTE: fingeRNAt considers all three abovementioned Pi - stacking interactions' types.

7. Ion-mediated interactions

Geometric rules:

  • |ligand's nitrogen/oxygen/sulphur - ion| <= X
  • |nucleic acid's nitrogen/oxygen - ion| <= X, where:
    • X = 3.2 Å for magnesium ion (Zheng et al., 2015)
    • X = 3.9 Å for potassium ion (Zheng et al., 2008)
    • X = 3.6 Å for sodium ion (Zheng et al., 2008)
    • X = 3.5 Å for other ions (Zheng et al., 2008)

8. Water-mediated interactions

NOTE: Only if fingeRNAt was called with -h2o parameter.

Geometric rules:

  • |ligand's hydrogen bond donor/acceptor - water (oxygen)| <= 3.5 Å (Poornima & Dean, 1995)
  • |nucleic acid's hydrogen bond donor/acceptor - water (oxygen)| <= 3.5 Å (Poornima & Dean, 1995)

9. Lipophilic interactions

Geometric rule:

  • |nucleic acid's carbon - ligand's lipophilic atom| <= 4.0 Å (Padroni et al., 2020)