Epik: A software program for pKa prediction and protonation state generation for drug-like molecules

Journal of Computer-Aided Molecular Design

Volumn 21, Issue 12, 2007, Pages 681-691

  Shelley, John C ^a   Cholleti, Anuradha ^b   Frye, Leah L ^a   Greenwood, Jeremy R ^c   Timlin, Mathew R ^a   Uchimaya, Makoto ^a  

^a Hansa Research   (United States)

^b D E Shaw India Software Private Limited   (India)

^c GAL Manufacturing Company   (United States)

Author keywords

Hammett and Taft (HT) equations; Ionization; Mesomers; pKa; Protonationstate; Tautomerization; Tautomers

Indexed keywords

BINDING ENERGY; DRUG DELIVERY; FORECASTING; IONIZATION; LIGANDS; PROTONATION;

HAMMETT AND TAFT EQUATION; MESOMER; MOLECULAR MODELING STUDIES; PKA; PROTONATION STATE; PROTONATIONSTATE; SOFTWARE PROJECT; STATE GENERATIONS; TAUTOMER; TAUTOMERIZATIONS;

MOLECULES;

DRUG;

ARTICLE; BINDING AFFINITY; CELL MEMBRANE PERMEABILITY; COMPUTER PROGRAM; DRUG CONFORMATION; DRUG PENETRATION; DRUG RESEARCH; DRUG SOLUBILITY; IONIZATION; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PKA; PREDICTION; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTON TRANSPORT; SURFACE CHARGE;

EID: 37749011993     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-007-9133-z     Document Type: Article

References (23)

1. Epik 1.5 (2007) Schrödinger, LLC, New York, NY
2. Perrin DD, Dempsy B, Sergeant EP (1981) pKa prediction for organic acids and bases. Chapman and Hall, London
3. LigPrep 2.1 (2007) Schrödinger, LLC, New York, NY
4. a values
5. ACD: http://www.acdlabs.com/products/phys_chem_lab/
6. ChemAxon: http://www.chemaxon.com/product/pka.html
7. Sparc software: http://www.epa.gov/ATHENS/publications/reports/ EPA_600_R_03_033.pdf
8. Klicic JJ, Friesner RA, Liu S-Y, Guida WCJ (2002) Phys Chem A 106, 1327 http://www.schrodinger.com
9. http://www.chemsilico.com/CS_products/products.html
10. SMARTS, SMiles ARbitrary Target Specification, is a registered trademark of Daylight Chemical Information Systems
11. Jaffé HH (1953) Chem Rev 53:191
12. Clark J, Perrin DD (1964) Quart Rev 18:295
13. Longuet-Higgins HC (1950) J Chem Phys 18:265. ibid. 275. ibid. 283
14. Perrin DD (1965) J Am Chem Soc 5590
15. Maestro 8.0 (2007) Schrödinger, LLC, New York, NY
16. Hägele G, Holzgrabe U (1999) In: Holzgrabe U, Wawer I, Diehl B (eds), NMR spectroscopy in drug development and analysis. Wiley-VCH, Weinheim Germany, pp 61-76
17. Jaguar 7.0 (2007) Schrödinger, LLC, New York, NY
18. Hansch C, Leo A, Hoekman D (1995) Exploring QSAR, hyrdophobic, electronic and steric constants. American Chemical Society, Washington, DC
19. Serjeant EP, Dempsey B (1979) Ionization constants of organic acids in aqueous solution. Pergamon Press, Oxford England
20. Perrin DD (1965) Dissociation constants of organic bases in aqueous solution. Butterworths, London
21. Perrin DD (1972) Dissociation constants of organic bases in aqueous solution: Supplement 1972. Butterworths, London
22. CrossFire Beilstein, version 7.0; MDL Information Systems GmbH, Frankfurt am Main, Germany (http://www.mdl.com)
23. DrugBank http://redpoll.pharmacy.ualberta.ca/drugbank/