MERA descriptors

See also full list of MERA descriptors as well as MERSY descriptors

Authors:

Maria Grishina maria_grishina@modelchem.ru
Vladimir Potemkin pva@modelchem.ru
ModelChem Group [1]

Mera descriptors summary

Descriptor name	Description
VME	molecular volume, Å³
SME	molecular surface, Å²
SMEP	weighted positively charged surface, (sum for positively charged atoms; is atomic charge)
SMEN	weighted negatively charged surface, (sum for negatively charged atoms; is atomic charge)
SMED	$S M = E P =E2=88=92 S M E N$
SMEPR	fraction of positively charged area,
SMENR	fraction of negatively charged area,
SMEDR	$S M = E P R =E2=88=92 S M E N R$
ESMEP	weighted average positively charged area, <= img class=3D"confluence-embedded-image" src=3D"f47fca58bddd18e6f7c9cfe66351= 26f4" data-image-src=3D"/download/attachments/7012917/image2013-6-28%200%3A= 34%3A37.png?version=3D1&modificationDate=3D1372380291000&api=3Dv2" = width=3D"222" height=3D"52" />
ESMEN	weighted average negatively charged area, <= img class=3D"confluence-embedded-image" src=3D"9ae9a15f105048dafb32b5c7217c= ea4f" data-image-src=3D"/download/attachments/7012917/image2013-6-28%200%3A= 34%3A55.png?version=3D1&modificationDate=3D1372380309000&api=3Dv2" = width=3D"225" height=3D"52" />
ESMED	$E S = M E P =E2=88=92 E S M E N$
QSMEP	weighted average positive charge of surface,&nbs= p;
QSMEN	weighted average positive charge of surface,&nbs= p;
QSMED	$Q S = M E P =E2=88=92 Q S M E N$
d204	density of compound
DMo	dipole moment, $= D$
SPH	sphericity, the ratio of surface of sphere ( $S S) with the volume= equal to the molecular volume, and the molecular surface (S M):$
VOIN1	sum of atomic volumes, Å³
VOIN1R	VOIN1R =3D VOIN1/VME
VOIN2	sum of volumes of double overlaps of atomic sphe= res, Å³
VOIN2R	part of double overlaps in the molecular volume,=
VOIN3	sum of volumes of triple overlaps of atomic sphe= res, Å³
VOIN3R	part of triple overlaps in the molecular volume,=
VOIN4	sum of volumes of quadruple overlaps of atomic s= pheres, Å³
VOIN4R	part of quadruple overlaps in the molecular volu= me,
VOIN5	sum of volumes of fivefold overlaps of atomic sp= heres, Å³
VOIN5R	part of fivefold overlaps in the molecular volum= e,
VOIN6	sum of volumes of sixfold overlaps of atomic sph= eres, Å³
VOIN6R	part of sixfold overlaps in the molecular volume= ,
HIMERA	pKA
MI1	the minimal principal moment of inertia, a.u.
MI2	the middle principal moment of inertia, a.u.
MI3	the maximal principal moment of inertia, a.u.
IR1	the minimal principal inertial radius, Å
IR2	the middle principal inertial radius, Å
IR3	the maximal principal inertial radius, Å
SI12	the minimal principal inertial section, , Å²
SI13	the middle principal inertial section, , Å²
SI23	the maximal principal inertial section, , Å²
PI12	proportion of molecule in the space of principal= rotational invariants,
PI13	proportion of molecule in the space of principal= rotational invariants,
PI23	proportion of molecule in the space of principal= rotational invariants,
DISS1	dissymmetry about the first principal rotatio= nal invariant. The dissymmetry is calculated as the third moment (skewness)= , i.e. (N =E2=80=93 number= of atoms; $x i$ &nb= sp;is the first coordinate of $i <= em>t h$ atom in the space of principal rotati= onal invariants), Å³
DISS2	dissymmetry about the second principal rotati= onal invariant, (N =E2=80= =93 number of atoms; $y i =$ is the second coordinate of $i t h$ atom in the space of= principal rotational invariants), Å³
DISS3	dissymmetry about the third principal rotatio= nal invariant, (N =E2=80= =93 number of atoms; $z i =$ is the third coordinate of $= i t h$ atom in the space of = principal rotational invariants), Å³

References

V.A. Potemkin, E.V. Bartashevich, and A.V. Belik A New Approach to Pred= icting the Thermodynamic Parameters of Substances from Molecular Characteri= stics// Russ. J. Phys. Chem.- 1996.- V. 70.- No. 3. P. 411 =E2=80=93 416.
Potemkin V. A., Bartashevich E. V., Grishina M. A., Guccione S. An Alte= rnative Method for 3D-QSAR and the Alignment of Molecular Structures: BiS (= Biological Substrate Search). In: Rational Approaches to Drug Design, H.-J.= Holtje, W.Sippl (Eds.). Barcelona: Prous Science Publishers, 2001.- P. 349 = =E2=80=93 353.
Potemkin V.A., Grishina M.A., Belik A.V., Chupakhin O.N. Quantitative R= elationship Between Structure and Antibacterial Activity of Quinolone Deriv= atives// Pharm. Chem. J.- 2002.- V. 36.- No. 1.- P. 22 =E2=80=93 25.
E.V. Bartashevich, V.A. Potemkin, M.A. Grishina, A.V. Belik A Method fo= r Multiconformational Modeling of the Three Dimensional Shape of a Molecule= // Journal of Structural Chemistry. =E2=80=93 2002.- V43. =E2=80=93 N. 6.-= P. 1033 =E2=80=93 1039.
M. A. Grishina, E. V. Bartashevich, V.A. Potemkin, A. V. Belik. Genetic= Algorithm for Predicting Structures and Properties of Molecular Aggregates= in Organic Substances// Journal of Structural Chemistry .- 2002. =E2=80=93= V.43.- N6.- p. 1040-1044.
V.A. Potemkin, R. M. Arslambekov, E. V. Bartashevich, M. A. Grishina, A= . V. Belik, S. Perspicace and S. Guccione. Multiconformational Method for A= nalyzing the Biological Activity of Molecular Structures// Journal of Struc= tural Chemistry.- 2002. =E2=80=93 V.43.- N 6. =E2=80=93 P. 1045-1049.
Mikuchina K., Potemkin V., Grishina M., Laufer S. 3D QSAR analysis and = pharmacophore modelling of p38 MAP kinase inhibitors using BiS algorithm// = Arch. Pharm. Pharm. Med. Chem.- 2002.- V. 335.- N 1.- P. C74.
Potemkin V.A., Grishina M.A., Fedorova O.V., Rusinov G.L., Ovchinnikova= I.G., Ishmetova R.I. Theoretical Investigation of the Antituberculous Acti= vity of Membranotropic Podands. // Pharm. Chem. J. 2003, V. 37, ? 9, pp. 46= 8-472.
Sinyaev A.A., Grishina M.A., Potemkin V.A. Theoretical study of solvent= influence on the regiospecificity of the reaction of 3-phenyl-s-tetrazine = with ketene-N,N-aminal// ARKIVOC.- 2004.- V. XI.- P. 43 =E2=80=93 52.
Potemkin V.A., Krasnov V.P., Levit G.L., Bartashevich E.V., Andreeva I.= N., Kuzminsky M.B., Anikin N.A., Charushin V.N., Chupakhin O.N. Kinetic res= olution of (±)-2,3-dihydro-3-methyl-4H-1,4-benzoxazine in the reacti= on with (S)-naproxen chloride: a theoretical study// Mendeleev Commun.- 200= 4.- Vol. 14.- ? 2.- P. 69 - 71.
V. A. Potemkin, M. A. Grishina, E. V. Bartachevich, T. Yu. Zrakova and = A. A. Pogrebnoi. Modeling the Interaction of Human Cytochrome P4502E1 with = Substrates// Biofizika.- 2005.- V. 50.- N 3.-pp. 378-381.
Grishina M.A., A.A. Pogrebnoi, V. A., Potemkin and T. Yu. Zrakova. Theo= retical study of the substrate specificity of cytochrome P-450 isoforms// P= harmaceutical Chemistry Journal.- 2005.- V. 39.- N 10
Grishina M.A., V.A. Potemkin, E. V. Bartashevich, A. N. Sinyaev, G. L. = Rusinov, N. I. Latosh, I. N. Ganebnykh, O. V. Koryakova and R. I. Ishmetova= . Modeling of 1,2,4,5-tetrazine complexes with organic amines//Journal of S= tructural Chemistry.- 2006.-V. 47.- N 6.
V.A. Potemkin, M.A. Grishina and E. V. Bartashevich. Modeling of drug m= olecule orientation within a receptor cavity in the BiS algorithm framework= // Journal of Structural Chemistry. 2007.-V. 48.- N 1.-P.155-160.
Potemkin V.A., Bartashevich E.V., Byler K., Clark T. Combined theoretic= al study of 5-HT1A-receptor agonists// Materialen zum wissenschaftlichen Se= minar des =E2=80=9CMichail Lomonosov=E2=80=9D-Programs 2006/07.- 16 =E2=80= =93 17 April, Moskau.- Moscow, 2007.- P. 181 =E2=80=93 183.
Grishina M.A., Bartashevich E.V., Pereyaslavskaya E.S. and Potemkin V.A= . A Novel Techniques for Virtual Discovery for Study of Multistage Bioproce= sses// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 27.
Pereyaslavskaya E.S., Potemkin V.A., Grishina M.A., Bartashevich E.V. T= he analysis of pharmacophoric parts of DHFR =E2=80=93 inhibitors using 3D-Q= SAR algorithm BiS/MC and X-ray data// Drugs of the Future.- 2007.- Vol. 32,= Suppl. A.- P. 87.
Grishina M.A., Potemkin V.A. A novel approach to pattern recognition fo= r drugs// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 112.
Potemkin V., Grishina M.A. A novel technique for virtual discovery for = study of multistage bioprocesses// 234th ACS National Meeting.- Boston, Aug= ust 19-23, 2007.- Book of Abstr.- P. COMP253.
Bartashevich E., Potemkin V. 3-D-QSAR Combined theoretical study of 5-H= T1A-receptor agonists// 234th ACS National Meeting.- Boston, August 19-23, = 2007.- Book of Abstr.- P. COMP349.
Grishina M.A., Potemkin V., Pereyaslavskaya E.S. A new paradigm for pat= tern recognition of drugs// 234th ACS National Meeting.- Boston, August 19-= 23, 2007.- Book of Abstr.- P. COMP414.
Kuzmicheva G.A., Eroshkin A.M., Potemkin V.A., Jayanna P.K., Petrenko V= .A. Modulating Affinity of Landscape Phage Nanoparticles by Mutagenesis of = the Major Coat Protein. In: Nanotechnology 2008: Life Sciences, Medicine &a= mp; Bio Materials - Vol. 2.- Boston, 2008.- P. 442 =E2=80=93 445.
Potemkin V.A., Grishina M.A. A new paradigm for pattern recognition of = drugs// Journal of Computer Aided Molecular Design.- 2008.- 22.-P. 489-505.=
Kuzmicheva G.A., Eroshkin A.M., Potemkin V.A., Jayanna P.K., Petrenko V= .A. Modulating Affinity of Landscape Phage Nanoparticles by Mutagenesis of = the Major Coat Protein// Nanotechnology 2008: Life Sciences, Medicine &= Bio Materials - Technical Proceedings of the 2008 NSTI Nanotechnology Conf= erence and Trade Show June 1 =E2=80=93 5, 2008.- Vol. 2.- Boston, 2008.- P.= 442 =E2=80=93 445.
M.A. Grishina, V.A. Potemkin, A.A. Pogrebnoi and N.N. Ivshina. A study = of conformational states of substrates of isoform 3A4 of cytochrome P450// = Biofizika.- 2008. =E2=80=93 V. 53.- N 5 .- P. 355-360.
E.S. Pereyaslavskaya, V.A. Potemkin, E.V. Bartashevich, M.A Grishina, G= .L. Rusinov, O.V. Fedorova, M.S. Zhidovinova, I.G. Ovchinnikova. Theoretica= l investigation of the antituberculosis activity of compounds of the dihydr= opyrimidine series // Pharmaceutical Chemistry Journal.- 2008 .- V.42.- N 1= 1.-P 622-625.
V. Potemkin, M. Grishina. Principles for 3D/4D QSAR classification of d= rugs // Drug discovery today.- 2008.- V.13. N21/22.-P. 952-959.
A.A. Pogrebnoy, M.A. Grishina, V.A. Potemkin, Modeling of complexes bet= ween cytochrome P450 1A2 and substrates// J. Struct. Chem.- 2009.- V. 50.- = N 5. P. 852 =E2=80=93 858.
Potemkin V.A., Pogrebnoy A.A., Grishina M.A. Technique for Energy Decom= position in the Study of =E2=80=9CReceptor-Ligand=E2=80=9D Complexes// J. C= hem. Inf. Model.-?2009.- Vol. 49.- ? 6.- P. 1389 =E2=80=93 1406.
Kuzmicheva G.A., Jayanna P.K., Eroshkin A.M., Grishina M.A., Pereyaslav= skaya E.S., Potemkin V.A., Petrenko V.A. Mutations in fd phage major coat p= rotein modulate affinity of the displayed peptide// Protein Engineering Des= ign and Selection, 2009.- Vol. 22(10).- P. 631 =E2=80=93 639.

MERA descriptors

Further reading

References