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

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Mera descriptors summary

Descriptor nameDescription
VMEmolecular volume, Å3
SMEmolecular surface, Å2
SMEPweighted positively charged surface,  (sum for positively charged atoms;  is atomic charge)
SMENweighted negatively charged surface,  (sum for negatively charged atoms;  is atomic charge)
SMEDSMEP − SMEN
SMEPRfraction of positively charged area, 
SMENRfraction of negatively charged area, 
SMEDRSMEPR − SMENR
ESMEPweighted average positively charged area, 
ESMENweighted average negatively charged area, 
ESMEDESMEP − ESMEN
QSMEPweighted average positive charge of surface, 
QSMENweighted average positive charge of surface, 
QSMEDQSMEP − QSMEN
d204density of compound 
DModipole moment, D
SPHsphericity, the ratio of surface of sphere (SS) with the volume equal to the molecular volume, and the molecular surface (SM): 
VOIN1sum of atomic volumes, Å3
VOIN1RVOIN1R = VOIN1/VME
VOIN2sum of volumes of double overlaps of atomic spheres, Å3
VOIN2Rpart of double overlaps in the molecular volume, 
VOIN3sum of volumes of triple overlaps of atomic spheres, Å3
VOIN3Rpart of triple overlaps in the molecular volume, 
VOIN4sum of volumes of quadruple overlaps of atomic spheres, Å3
VOIN4Rpart of quadruple overlaps in the molecular volume, 
VOIN5sum of volumes of fivefold overlaps of atomic spheres, Å3
VOIN5Rpart of fivefold overlaps in the molecular volume, 
VOIN6sum of volumes of sixfold overlaps of atomic spheres, Å3
VOIN6Rpart of sixfold overlaps in the molecular volume, 
HIMERApKA
MI1the minimal principal moment of inertia, a.u.
MI2the middle principal moment of inertia, a.u.
MI3the maximal principal moment of inertia, a.u.
IR1the minimal principal inertial radius, Å
IR2the middle principal inertial radius, Å
IR3the maximal principal inertial radius, Å
SI12the minimal principal inertial section, , Å2
SI13the middle principal inertial section, , Å2
SI23the maximal principal inertial section, , Å2
PI12proportion of molecule in the space of principal rotational invariants, 
PI13proportion of molecule in the space of principal rotational invariants, 
PI23proportion of molecule in the space of principal rotational invariants, 
DISS1

dissymmetry about the first principal rotational invariant. The dissymmetry is calculated as the third moment (skewness), i.e.  

(N – number of atoms;xi is the first coordinate of ith atom in the space of principal rotational invariants), Å3

DISS2

dissymmetry about the second principal rotational invariant,  

(N – number of atoms; yi is the second coordinate of ith atom in the space of principal rotational invariants), Å3

DISS3

dissymmetry about the third principal rotational invariant,  

(N – number of atoms; zi is the third coordinate of ith atom in the space of principal rotational invariants), Å3

Further reading

  1. Grishina M., Potemkin V. Strategies for Virtual Drug Discovery. Wiley & Sons, NJ, 2010, 512 pp. (in press)
  2. Potemkin V., Grishina M. In silico techniques for . Wiley & Sons, Chichester, 2010, 412 pp. (in press)

References

  1. V.A. Potemkin, E.V. Bartashevich, and A.V. Belik A New Approach to Predicting the Thermodynamic Parameters of Substances from Molecular Characteristics// Russ. J. Phys. Chem.- 1996.- V. 70.- No. 3. P. 411 – 416.
  2. Potemkin V. A., Bartashevich E. V., Grishina M. A., Guccione S. An Alternative 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 – 353.
  3. Potemkin V.A., Grishina M.A., Belik A.V., Chupakhin O.N. Quantitative Relationship Between Structure and Antibacterial Activity of Quinolone Derivatives// Pharm. Chem. J.- 2002.- V. 36.- No. 1.- P. 22 – 25.
  4. E.V. Bartashevich, V.A. Potemkin, M.A. Grishina, A.V. Belik A Method for Multiconformational Modeling of the Three Dimensional Shape of a Molecule // Journal of Structural Chemistry. – 2002.- V43. – N. 6.- P. 1033 – 1039.
  5. 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. – V.43.- N6.- p. 1040-1044.
  6. V.A. Potemkin, R. M. Arslambekov, E. V. Bartashevich, M. A. Grishina, A. V. Belik, S. Perspicace and S. Guccione. Multiconformational Method for Analyzing the Biological Activity of Molecular Structures// Journal of Structural Chemistry.- 2002. – V.43.- N 6. – P. 1045-1049.
  7. 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.
  8. Potemkin V.A., Grishina M.A., Fedorova O.V., Rusinov G.L., Ovchinnikova I.G., Ishmetova R.I. Theoretical Investigation of the Antituberculous Activity of Membranotropic Podands. // Pharm. Chem. J. 2003, V. 37, ? 9, pp. 468-472.
  9. 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 – 52.
  10. 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 resolution of (±)-2,3-dihydro-3-methyl-4H-1,4-benzoxazine in the reaction with (S)-naproxen chloride: a theoretical study// Mendeleev Commun.- 2004.- Vol. 14.- ? 2.- P. 69 - 71.
  11. 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.
  12. Grishina M.A., A.A. Pogrebnoi, V. A., Potemkin and T. Yu. Zrakova. Theoretical study of the substrate specificity of cytochrome P-450 isoforms// Pharmaceutical Chemistry Journal.- 2005.- V. 39.- N 10
  13. 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 Structural Chemistry.- 2006.-V. 47.- N 6.
  14. V.A. Potemkin, M.A. Grishina and E. V. Bartashevich. Modeling of drug molecule orientation within a receptor cavity in the BiS algorithm framework// Journal of Structural Chemistry. 2007.-V. 48.- N 1.-P.155-160.
  15. Potemkin V.A., Bartashevich E.V., Byler K., Clark T. Combined theoretical study of 5-HT1A-receptor agonists// Materialen zum wissenschaftlichen Seminar des “Michail Lomonosov”-Programs 2006/07.- 16 – 17 April, Moskau.- Moscow, 2007.- P. 181 – 183.
  16. Grishina M.A., Bartashevich E.V., Pereyaslavskaya E.S. and Potemkin V.A. A Novel Techniques for Virtual Discovery for Study of Multistage Bioprocesses// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 27.
  17. Pereyaslavskaya E.S., Potemkin V.A., Grishina M.A., Bartashevich E.V. The analysis of pharmacophoric parts of DHFR – inhibitors using 3D-QSAR algorithm BiS/MC and X-ray data// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 87.
  18. Grishina M.A., Potemkin V.A. A novel approach to pattern recognition for drugs// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 112.
  19. Potemkin V., Grishina M.A. A novel technique for virtual discovery for study of multistage bioprocesses// 234th ACS National Meeting.- Boston, August 19-23, 2007.- Book of Abstr.- P. COMP253.
  20. Bartashevich E., Potemkin V. 3-D-QSAR Combined theoretical study of 5-HT1A-receptor agonists// 234th ACS National Meeting.- Boston, August 19-23, 2007.- Book of Abstr.- P. COMP349.
  21. Grishina M.A., Potemkin V., Pereyaslavskaya E.S. A new paradigm for pattern recognition of drugs// 234th ACS National Meeting.- Boston, August 19-23, 2007.- Book of Abstr.- P. COMP414.
  22. 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 & Bio Materials - Vol. 2.- Boston, 2008.- P. 442 – 445.
  23. 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.
  24. 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 Conference and Trade Show June 1 – 5, 2008.- Vol. 2.- Boston, 2008.- P. 442 – 445.
  25. 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. – V. 53.- N 5 .- P. 355-360.
  26. E.S. Pereyaslavskaya, V.A. Potemkin, E.V. Bartashevich, M.A Grishina, G.L. Rusinov, O.V. Fedorova, M.S. Zhidovinova, I.G. Ovchinnikova. Theoretical investigation of the antituberculosis activity of compounds of the dihydropyrimidine series // Pharmaceutical Chemistry Journal.- 2008 .- V.42.- N 11.-P 622-625.
  27. V. Potemkin, M. Grishina. Principles for 3D/4D QSAR classification of drugs // Drug discovery today.- 2008.- V.13. N21/22.-P. 952-959.
  28. A.A. Pogrebnoy, M.A. Grishina, V.A. Potemkin, Modeling of complexes between cytochrome P450 1A2 and substrates// J. Struct. Chem.- 2009.- V. 50.- N 5. P. 852 – 858.
  29. Potemkin V.A., Pogrebnoy A.A., Grishina M.A. Technique for Energy Decomposition in the Study of “Receptor-Ligand” Complexes// J. Chem. Inf. Model.-?2009.- Vol. 49.- ? 6.- P. 1389 – 1406.
  30. Kuzmicheva G.A., Jayanna P.K., Eroshkin A.M., Grishina M.A., Pereyaslavskaya E.S., Potemkin V.A., Petrenko V.A. Mutations in fd phage major coat protein modulate affinity of the displayed peptide// Protein Engineering Design and Selection, 2009.- Vol. 22(10).- P. 631 – 639.