Comparative binding energy analysis (COMBINE)

First description of the COMBINE analysis method :

Prediction of drug binding affinities by comparative binding energy analysis.
Ortiz AR, Pisabarro MT, Gago F, Wade RC
J Med Chem38p2681-91(1995 Jul 7)

  1. A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure-activity relationships using comparative binding energy (COMBINE) analysis.
    Coderch C, Tang Y, Klett J, Zhang SE, Ma YT, Shaorong W, Matesanz R, Pera B, Canales A, Jiménez-Barbero J, Morreale A, Díaz JF, Fang WS, Gago F
    Org Biomol Chem11p3046-56(2013 May 14)
  2. Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE).
    Liu S, Fu R, Cheng X, Chen SP, Zhou LH
    BMC Struct Biol12p21(2012 Aug 27)
  3. Histone deacetylase inhibitors: structure-based modeling and isoform-selectivity prediction.
    Silvestri L, Ballante F, Mai A, Marshall GR, Ragno R
    J Chem Inf Model52p2215-35(2012 Aug 27)
  4. Comparative binding energy (COMBINE) analysis supports a proposal for the binding mode of epothilones to β-tubulin.
    Coderch C, Klett J, Morreale A, Fernando Díaz J, Gago F
    ChemMedChem7p836-43(2012 May)
  5. Quantum mechanical pairwise decomposition analysis of protein kinase B inhibitors: validating a new tool for guiding drug design.
    Zhang X, Gibbs AC, Reynolds CH, Peters MB, Westerhoff LM
    J Chem Inf Model50p651-61(2010 Apr 26)
  6. Comparative binding energy analysis for binding affinity and target selectivity prediction.
    Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC
    Proteins78p135-53(2010 Jan)
  7. Distinct interactions of 2'- and 3'-O-(N-methyl)anthraniloyl-isomers of ATP and GTP with the adenylyl cyclase toxin of Bacillus anthracis, edema factor.
    Suryanarayana S, Wang JL, Richter M, Shen Y, Tang WJ, Lushington GH, Seifert R
    Biochem Pharmacol78p224-30(2009 Aug 1)
  8. Key residues controlling binding of diverse ligands to human cytochrome P450 2A enzymes.
    DeVore NM, Smith BD, Wang JL, Lushington GH, Scott EE
    Drug Metab Dispos37p1319-27(2009 Jun)
  9. An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors.
    Nicolotti O, Miscioscia TF, Carotti A, Leonetti F, Carotti A
    J Chem Inf Model48p1211-26(2008 Jun)
  10. Masamoto Arakawaa, Kiyoshi Hasegawab, Kimito Funatsu: Tailored scoring function of Trypsin–benzamidine complex using COMBINE descriptors and support vector regression. Chemometrics and Intelligent Laboratory Systems, Volume 92, Issue 2, 15 July 2008, Pages 145-151.
  11. COMBINE analysis of the specificity of binding of Ras proteins to their effectors.
    Tomić S, Bertosa B, Wang T, Wade RC
    Proteins67p435-47(2007 May 1)
  12. Whither combine? New opportunities for receptor-based QSAR.
    Lushington GH, Guo JX, Wang JL
    Curr Med Chem14p1863-77(2007)
  13. Martin B. Peters, Kenneth M. Merz Jr.: Semiempirical Comparative Binding Energy Analysis (SE-COMBINE) of a Series of Trypsin Inhibitors. J. Chem. Theory Comput., 2006, 2 (2), pp 383–399.
  14. Computational approaches to model ligand selectivity in drug design.
    Ortiz AR, Gomez-Puertas P, Leo-Macias A, Lopez-Romero P, Lopez-Viñas E, Morreale A, Murcia M, Wang K
    Curr Top Med Chem6p41-55(2006)
  15. Marta Murcia, Antonio Morreale, Angel R. Ortiz: Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets. J. Med. Chem., 2006, 49 (21), pp 6241–6253. link
  16. Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.
    Kmunícek J, Hynková K, Jedlicka T, Nagata Y, Negri A, Gago F, Wade RC, Damborský J
    Biochemistry44p3390-401(2005 Mar 8)
  17. How optimal are the binding energetics of barnase and barstar?
    Wang T, Tomic S, Gabdoulline RR, Wade RC
    Biophys J87p1618-30(2004 Sep)
  18. Rebecca C. Wade, Stefan Henrich, Ting Wang: Using 3D protein structures to derive 3D-QSARs. Drug Discovery Today: Technologies, Volume 1, Issue 3, December 2004, Pages 241-246.
  19. Comparative structural and energetic analysis of WW domain-peptide interactions.
    Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC
    J Mol Biol344p865-81(2004 Nov 26)
  20. Computational studies of COX-2 inhibitors: 3D-QSAR and docking.
    Kim HJ, Chae CH, Yi KY, Park KL, Yoo SE
    Bioorg Med Chem12p1629-41(2004 Apr 1)
  21. Jiri Damborsky, Jan Kmunicek, Tomas Jedlicka,Santos Luengo, Federico Gago, Angel R. Ortiz and Rebecca C. Wade: Rational Re-design of Haloalkane Dehalogenases Guided by Comparative Binding Energy Analysis. In “Enzyme functionality: Design, Engineering and Screening”, Ed. A. Svendsen, Marcel Dekker, New York, ISBN: 0-8247-4709-7 (2004) pp79-96.
  22. Ting Wang, Rebecca C. Wade: COMBINE 3D-QSAR Analysis of Influenza Neuraminidase Inhibitors. In: “Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships”, Eds. Holtje, H-D., Sippl,W. (2001), Prous Science S.A., Barcelona, pp78-82.
  23. Rebecca C. Wade: Derivation of QSARs using 3D structural models of protein-ligand complexes. In: “Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships”, Eds. Holtje, H-D., Sippl,W. (2001), Prous Science S.A., Barcelona, pp23-28.
  24. Sanja Tomica, Rebecca C. Wade: COMBINE Analysis of Nuclear Receptor-DNA Binding Specificity: Comparison of Two Sets of Data. CROATICA CHEMICA ACTA CCACAA 74 (2) 295-314 (2001), ISSN-0011-1643 CCA-2733 Original Scientific Paper.
  25. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
    Kmunícek J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborský J
    Biochemistry40p8905-17(2001 Jul 31)
  26. Sanja Tomic,Lennart Nilsson, Rebecca C. Wade: Nuclear Receptor−DNA Binding Specificity: A COMBINE and Free−Wilson QSAR Analysis. J. Med. Chem., 2000, 43 (9), pp 1780–1792.
  27. M. Pastor, F. Gago, G. Cruciani: Comparative binding energy (COMBINE) analysis on a series of glycogen phosphorylase inhibitors: comparison with GRID/GOLPE methods. 2000
  28. 3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands.
    Lozano JJ, Pastor M, Cruciani G, Gaedt K, Centeno NB, Gago F, Sanz F
    J Comput Aided Mol Des14p341-53(2000 May)
  29. Kiyoshi Hasegawa, Toshiro Kimura, Kimito Funatsu: GA Strategy for Variable Selection in QSAR Studies: Enhancement of Comparative Molecular Binding Energy Analysis by GA-Based PLS Method. Quantitative Structure-Activity Relationships, 18 (3) 262–272, July 1999.
  30. Rebecca C. Wade, A. R. Oritz, F. Gago: Comparative binding energy analysis. Perspectives in Drug Discovery and Design, Volumes 9-11, January 1998 , 19-34(16).
  31. Prediction of drug binding affinities by comparative binding energy analysis.
    Ortiz AR, Pisabarro MT, Gago F, Wade RC
    J Med Chem38p2681-91(1995 Jul 7)