Molecular properties

"The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment." (Handbook of Molecular Descriptors, R.Todeschini and V.Consonni, Wiley-VCH, 2000).

Molecular descriptors play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, health research and quality control, they being obtained when molecules are transformed into a molecular representation allowing some mathematical treatment. Many molecular descriptors have been proposed derived from different theories and approaches with the aim of predicting biological and physico-chemical properties of molecules [R.Todeschini and V.Consonni, Handbook of Molecular Descriptors, Wiley-VCH, Weinheim (GER), 2000].

The information content of a molecular descriptor depends on the kind of molecular representation that is used and on the defined algorithm for its calculation. There are simple molecular descriptors derived by counting some atom-types or structural fragments in the molecule, other derived from algorithms applied to a topological representation (molecular graph) and usually called topological or 2D-descriptors, and there are molecular descriptors derived from a geometrical representation that are called geometrical or 3D-descriptors.

All the molecular descriptors must contain, to varying extents, chemical information, must satisfy some basic invariance properties and general requirements, and must be derived from well-established procedures which enable molecular descriptors to be calculated for any set of molecules. It is obvious – almost trivial - that a single descriptor or a small number of descriptors cannot wholly represent the molecular complexity or model all the physico-chemical responses and biological interactions. As a consequence, although we must get used to living with approximate models (nothing is perfect!), we have to keep in mind that "approximate" is not a synonym of "useless".

The field of molecular descriptors is strongly interdisciplinary and involves a variety of different theories. For the definition of molecular descriptors, a knowledge of algebra, graph theory, information theory, computational chemistry, theories of organic reactivity and physical chemistry is usually required, although at different levels. For the use of the molecular descriptors, a knowledge of statistics, chemometrics, and the principles of the QSAR/QSPR approaches is necessary in addition to the specific knowledge of the problem.

The molecular descriptors/properties calculated by dProperties can be divided in three blocks:

ID	Label	Description
1	MW	molecular weight
2	nAT	number of atoms
3	nBT	number of rotatable bonds
4	RBN	number of rotatable bonds
5	nDB	number of double bonds
6	nAB	number of aromatic bonds
7	nH	number of Hydrogen atoms
8	nC	number of Carbon atoms
9	nN	number of Nitrogen atoms
10	nO	number of Oxygen atoms
11	nHet	number of heteroatoms
12	nX	number of halogen atoms
13	nCIC	number of rings (cyclomatic number)
14	nHDon	number of donor atoms for H-bonds (N and O)
15	nHAcc	number of acceptor atoms for H-bonds (N,O,F)
16	Uc	unsaturation count
17	Ui	unsaturation index
18	Hy	hydrophilic factor
19	AMR	Ghose-Crippen molar refractivity
20	TPSA(NO)	topological polar surface area using N,O polar contributions
21	TPSA(Tot)	topological polar surface area using N,O,S,P polar contributions
22	MLOGP	Moriguchi octanol-water partition coeff. (logP)
23	MLOGP2	squared Moriguchi octanol-water partition coeff. (logP2)
24	ALOGP	Ghose-Crippen octanol-water partition coeff. (logP)
25	ALOGP2	squared Ghose-Crippen octanol-water partition coeff. (logP2)
26	SAtot	total surface area from P_VSA-like descriptors
27	SAacc	surface area of acceptor atoms from P_VSA-like descriptors
28	SAdon	surface area of donor atoms from P_VSA-like descriptors
29	Vx	McGowan volume
30	VvdwMG	van der Waals volume from McGowan volume
31	VvdwZAZ	van der Waals volume from Zhao-Abraham-Zissimos equation
32	PDI	packing density index
33	BLTF96	Verhaar Fish base-line toxicity from MLOGP (mmol/l)
34	BLTD48	Verhaar Daphnia base-line toxicity from MLOGP (mmol/l)
35	BLTA96	Verhaar Algae base-line toxicity from MLOGP (mmol/l)
36	Ro5	Lipinski Rule of 5
37	DLS_01	modified drug-like score from Lipinski (4 rules)
38	DLS_02	modified drug-like score from Oprea et al. (6 rules)
39	DLS_03	modified drug-like score from Walters et al. (6 rules)
40	DLS_04	modified drug-like score from Chen et al. (7 rules)
41	DLS_05	modified drug-like score from Zheng et al. (2 rules)
42	DLS_06	modified drug-like score from Rishton (6 rules)
43	DLS_07	modified drug-like score from Veber et al. (2 rules)
44	DLS_cons	DRAGON consensus drug-like score
45	LLS_01	modified lead-like score from Congreve et al. (6 rules)
46	LLS_02	modified lead-like score from Monge et al. (8 rules)
47	CMC-80	Ghose-Viswanadhan-Wendoloski CMC drug-like index at 80%
48	CMC-50	Ghose-Viswanadhan-Wendoloski CMC drug-like index at 50%
49	Inflammat-80	Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 80%
50	Inflammat-50	Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 50%
51	Depressant-80	Ghose-Viswanadhan-Wendoloski antidepressant-like index at 80%
52	Depressant-50	Ghose-Viswanadhan-Wendoloski antidepressant-like index at 50%
53	Psychotic-80	Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 80%
54	Psychotic-50	Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 50%
55	Hypertens-80	Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 80%
56	Hypertens-50	Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 50%
57	Hypnotic-80	Ghose-Viswanadhan-Wendoloski hypnotic-like index at 80%
58	Hypnotic-50	Ghose-Viswanadhan-Wendoloski hypnotic-like index at 50%
59	Neoplastic-80	Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 80%
60	Neoplastic-50	Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 50%
61	Infective-80	Ghose-Viswanadhan-Wendoloski antiinfective-like index at 80%
62	Infective-50	Ghose-Viswanadhan-Wendoloski antiinfective-like index at 50%