Skip to main content
SpringerLink
Log in

KRAKENX: software for the generation of alignment-independent 3D descriptors

  • Software Report
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

The KRAKENX software calculates a large variety of molecular descriptors based on quantum chemistry computations. The program supports over 2000 three-dimensional descriptors that are calculated from the output of different quantum chemistry packages. The current implementation supports semi-empirical MOPAC-based computations and primarily focuses on orientation-independent descriptors that have been discussed in the literature. The descriptor performance has been exemplified using a number of large and diverse datasets and can be seen to produce parsimonious linear models. The software can be run on multiple platforms and is available to academics free of charge.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  1. Karelson M, Lobanov VS, Katritzky AR (1996) Chem Rev 96(3):1027

    Article  CAS  Google Scholar 

  2. Le T, Epa VC, Burden FR, Winkler DA (2012) Chem Rev 112(5):2889

    Article  CAS  Google Scholar 

  3. Katritzky AR, Kuanar M, Slavov S, Hall CD, Karelson M, Kahn I, Dobchev DA (2010) Chem Rev 110(10):5714

    Article  CAS  Google Scholar 

  4. Pogliani L (2000) Chem Rev 100(10):3827

    Article  CAS  Google Scholar 

  5. Todeschini R, Consonni V (2010) Molecular Descriptors for Chemoinformatics, vol 41. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

    Google Scholar 

  6. Guha R, Willighagen E (2012) Curr Top Med Chem 12(18):1946

    Article  CAS  Google Scholar 

  7. Cramer RD, Patterson DE, Bunce JD (1988) J Am Chem Soc 110(18):5959

    Article  CAS  Google Scholar 

  8. Klebe G, Abraham U, Mietzner T (1994) J Med Chem 37(24):4130

    Article  CAS  Google Scholar 

  9. Tetko I, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV (2005) J Comput-Aided Mol Des 19 (6):453

    Article  CAS  Google Scholar 

  10. Li Z, Han L, Xue Y, Yap C, Li H, Jiang L, Chen Y (2007) Biotechnol Bioeng 97(2):389

    Article  CAS  Google Scholar 

  11. Jeliazkova N, Jeliazkov V (2011) J Cheminf 3(1):18

    Article  CAS  Google Scholar 

  12. Parasurf’10 academic version (2010) CEPOS Insilico Ltd. Erlangen, Germany

  13. Tosco P, Balle T (2011) J Mol Model 17(1):201

    Article  Google Scholar 

  14. Talete srl, dragon (software for molecular descriptor calculation) (2012). Version 6.0, http://www.talete.mi.it

  15. Codessa pro version 1.0 rc2 (2002). University of Florida: Gainesville, FL

  16. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L, Su Z, Perkins R, Tong W, Chem J (2008) Inf Model 48(7):1337

    Article  CAS  Google Scholar 

  17. Yap CW (2011) J Comp Chem 32(7):1466

    Article  CAS  Google Scholar 

  18. Cao DS, Xu QS, Hu QN, Liang YZ (2013) Bioinformatics 29(8):1092

    Article  CAS  Google Scholar 

  19. Melville JL, Hirst JD, Chem J (2007) Inf Model 47(2): 626

    Article  CAS  Google Scholar 

  20. Varnek A, Fourches D, Horvath D, Klimchuk O, Gaudin C, Vayer P, Solov’ev V, Hoonakker F, Tetko IV, Marcou G (2008) Curr Comp Aided-Drug Des 4(3):191

    Article  CAS  Google Scholar 

  21. García-Jacas CR, Marrero-Ponce Y, Acevedo-Martínez L, Barigye SJ, Valdés-Martinez JR, Contreras-Torres E (2014) J Comp Chem 35(18):1395

    Article  Google Scholar 

  22. Guha R, Howard MT, Hutchison GR, Murray-Rust P, Rzepa H, Steinbeck C, Wegner J, Willighagen EL, Chem J (2006) Inf Model 46(3):991

    Article  CAS  Google Scholar 

  23. Molecular operating environment (moe), 2013.08 (2015). Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7

  24. Hall LH, Kellog GE, Haney DN (2002) Molconn-Z version 4.00 user guide. Edusoft LC, La Jolla, CA

    Google Scholar 

  25. Cruciani G, Crivori P, Carrupt PA, Testa B (2000) J Mol Struc-THEOCHEM 503(1-2):17

    Article  CAS  Google Scholar 

  26. Liu J, Feng J, Young S, Chem J (2005) Inf Model 45:515

    Article  CAS  Google Scholar 

  27. Marvin 5.9.3 (2012). ChemAxon (http://www.chemaxon.com)

  28. Gece G (2008) Corros Sci 50(11):2981

    Article  CAS  Google Scholar 

  29. Dehmer M, Varmuza K, Bonchev D (2012) Statistical Modelling of Molecular Descriptors in QSAR/QSPR. Wiley-VCH Verlag GmbH & Co, KGaA, Weinheim

    Book  Google Scholar 

  30. Stewart JJP Mopac2012 version 14.142l (2012). Stewart Computational Chemistry, Colorado Springs, CO, USA, (http://OpenMOPAC.net)

  31. Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen E (2006) Curr Pharm Des 12(17):2111

    Article  CAS  Google Scholar 

  32. Csizmadia I (1976) Theory and Practice of MO Calculations on Organic Molecules. Progress in theoretical organic chemistry (Elsevier Scientific Pub. Co, Amsterdam, New York

    Google Scholar 

  33. Clementi E (1980) Computational Aspects for Large Chemical Systems Lecture Notes in Chemistry. Springer, Berlin Heidelberg

    Book  Google Scholar 

  34. McQuarrie DA (1985) Statistical Thermodynamics, University Science Books

  35. Akhiezer AI, Peletminskii SV, Ter Haar D (eds) (1981) Methods of Statistical Physics, International Series in Natural Philosophy, vol 104. Pergamon

  36. Osmiaowski K, Halkiewicz J, Radecki A, Kaliszan R (1985) J Chromatogr A 346:53

    Article  Google Scholar 

  37. Katritzky AR, Mu L, Karelson M (1996) J Chem Inf Model 36(6):1162

    CAS  Google Scholar 

  38. Clare BW, Supuran CT (1994) J Pharm Sci 83(6):768

    Article  CAS  Google Scholar 

  39. Stanton D, Jurs P (1990) Anal Chem 62:2323

    Article  CAS  Google Scholar 

  40. Aptula A, Kühne R, Ebert RU, Cronin M, Netzeva T, Schüürmann G (2003) Mol Inf 22(1):113

    CAS  Google Scholar 

  41. Turner DB, Willett P (2000) Eur J Med Chem 35(4):367

    Article  CAS  Google Scholar 

  42. Tuppurainen K (1999) SAR QSAR Environ Res 10(1):39

    Article  CAS  Google Scholar 

  43. Heritage T, Ferguson A, Turner D, Willett P (1998) Perspect. Drug Discov 381:9–11

    Google Scholar 

  44. Venkatraman V, Åstrand PO, Alsberg BK (2014) J Comput Chem 35(3):214

    Article  CAS  Google Scholar 

  45. Venkatraman V, Alsberg BK (2015) Dyes Pigment 114(0): 69

    Article  CAS  Google Scholar 

  46. Venkatraman V, Foscato M, Jensen VR, Alsberg BK (2015) J Mater Chem A 3:9851

    Article  CAS  Google Scholar 

  47. Bogdanov B, Nikolić S, Trinajstić N (1989) J Math Chem 3(3):299

    Article  CAS  Google Scholar 

  48. Todeschini R, Consonni V (2003). In: Gasteiger J (ed) Handbook of Chemoinformatics: From Data to Knowledge. Wiley-VCH Verlag GmbH, Weinheim, Germany

  49. Hemmer MC, Steinhauer V, Gasteiger J (1999) Vib Spectrosc 19(1):151

    Article  CAS  Google Scholar 

  50. Schuur JH, Selzer P, Gasteiger J (1996) J Chem Inf Model 36(2):334

    CAS  Google Scholar 

  51. Todeschini R, Vighi M, Provenzani R, Finizio A, Gramatica P (1996) Chemosphere 32(8):1527

    Article  CAS  Google Scholar 

  52. Klein CT, Kaiser D, Ecker G, Chem J (2004) Inf Model 44(1):200

    CAS  Google Scholar 

  53. Bajorath J (2004) Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery, Methods in Molecular Biology, vol 41. Humana Press

  54. Bultinck P, Langenaeker W, Carbó-Dorca R, Tollenaere JP (2003) J Chem Inf Model 43(2):422

    CAS  Google Scholar 

  55. Geladi P, Kowalski BR (1986) Anal Chim Acta 185(0):1

    Article  CAS  Google Scholar 

  56. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) J Am Chem Soc 107:3902

    Article  CAS  Google Scholar 

  57. Mevik BH, Wehrens R (2007) J Stat Softw 18(2):1

    Article  Google Scholar 

  58. Team RC (2015) R: A Language and Environment for Statistical Computing, Vienna, Austria. https://www.R-project.org/

  59. Chong IG, Jun CH (2005) Chemomtr Intell Lab 78(1-2):103

    Article  CAS  Google Scholar 

  60. Contrera JF, Matthews EJ, Benz RD (2003) Regul Toxicol Pharm 38(3):243

    Article  CAS  Google Scholar 

  61. Martin TM, Harten P, Venkatapathy R, Das S, Young DM (2008) Toxicol Mech Methods 18(2-3):251

    Article  CAS  Google Scholar 

  62. Martin TM, Young DM (2001) Chem Res Toxicol 14(10):1378

    Article  CAS  Google Scholar 

  63. Viswanath D, Ghosh T, Prasad D, Dutt N, Rani K (2007) Viscosity of Liquids: Theory, Estimation, Experiment and Data. Springer, Netherlands

    Google Scholar 

  64. Breiman L, Friedman JH, Olshen RA, Stone CJ (1984) Classification and Regression Trees. Wadsworth

  65. Liaw A, Wiener M (2002) R News 2(3):18

    Google Scholar 

  66. Melagraki G, Afantitis A (2013) Chemomtr Intell Lab 123:9

    Article  CAS  Google Scholar 

  67. Mansouri K, Ringsted T, Ballabio D, Todeschini R, Consonni V (2013) J Chem Inf Model 53(4):867

    Article  CAS  Google Scholar 

  68. Eide-Haugmo I (2011) Environmental impacts and aspects of absorbents used for co2 capture. Ph.D. thesis, Norges Teknisk-Naturvitenskapelige Universitet, Norway

  69. Brown BWE, Steven D, Tauler R (2009) Comprehensive chemometrics Chemical and biochemical data analysis. Elsevier

  70. Sanchez G (2013) DiscriMiner: Tools of the Trade for Discriminant Analysis. http://CRAN.R-project.org/package=DiscriMiner. R package version 0.1-29

Download references

Acknowledgments

The Norwegian Research Council (NFR) is acknowledged for financial support from the CLIMIT (Grant No. 233776). We also thank ChemAxon (http://www.chemaxon.com) for free academic use of the Marvin package.

Author information

Authors and Affiliations

  1. Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway

    Vishwesh Venkatraman & Bjørn Kåre Alsberg

Authors
  1. Vishwesh Venkatraman
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bjørn Kåre Alsberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bjørn Kåre Alsberg.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Venkatraman, V., Alsberg, B.K. KRAKENX: software for the generation of alignment-independent 3D descriptors. J Mol Model 22, 93 (2016). https://doi.org/10.1007/s00894-016-2957-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-016-2957-5

Keywords

Search

Navigation