Molecular description in chemical informatics

Molecular structure - // - > Properties (바로 Properties를 표현하긴 힘들다)

Molecular structure -> Representation -> Description -> Modeling -> Properties.

Description

Global descriptors

Based on the whole molecule
 - LogP

 - Volume
 - surface aeas (polar, non-polar)
 - Dipole moment
 - Refractive index, etc.

No problem with 3D alignment

No information about favorable interactions

Local descriptors

Describes a part of the molecule

 - Charges (pKa)

 - Hydrogen bond donors and acceptors

 - partial volumes (substituent)

Alignment dependent descriptors

Information about important parts for receptor

Scaffolds (common vs diverse)

1. LogP

https://en.wikipedia.org/wiki/Partition_coefficient

In the physical sciences, a partition-coefficient (P) or distribution-coefficient (D) is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium

값이 높을수록 hydrophobicity, 값이 낮을수록 hydrophilicity함.

2. Volume

3. surface aeas (polar, non-polar)

Volume도 중요하지만, Surface가 더 일반적.

compound가 Interaction할 때, 결국엔 표면에 있는 것이 작용하기 때문.

solvent-accessible surface area (SASA)

https://en.wikipedia.org/wiki/Accessible_surface_area

The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent.

Connolly surface를 SASA로 쓰기도 한다고 함.

The binding site is relatively small and hydrophobic, so the solvent-accessible surface area and the log P for an inhibitor should fall in the 450 to 650 Å2 and 2 to 6 ranges, respectively.

결합부위가 상대적으로 작고, hydrophobic 하기 때문에, SASA값과 logP 값은 450~650, 2~6 정도의 값을 가져야함

4. Dipole moment

5. Refractive index, etc.

주요 Molecular descriptor Table for A.A.

이 데이터를 주로 PCA를 이용해서 visualization 해준다.