Comparative binding energy analysis (COMBINE)

Description of original method:

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. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors.
   Peón A, Coderch C, Gago F, González-Bello C
   ChemMedChem8p740-7(2013 May)
3. 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)
4. 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)
5. 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)
6. 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)
7. 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)
8. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.
   Gil-Redondo R, Klett J, Gago F, Morreale A
   Proteins78p162-72(2010 Jan)
9. 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)
10. 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)
11. 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)
12. 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.
13. A conformational transition in the adenylyl cyclase catalytic site yields different binding modes for ribosyl-modified and unmodified nucleotide inhibitors.
    Wang JL, Guo JX, Zhang QY, Wu JJ, Seifert R, Lushington GH
    Bioorg Med Chem15p2993-3002(2007 Apr 15)
14. 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)
15. Whither combine? New opportunities for receptor-based QSAR.
    Lushington GH, Guo JX, Wang JL
    Curr Med Chem14p1863-77(2007)
16. 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.
17. 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)
18. Binding affinity prediction of non-peptide inhibitors of HIV-1 protease using COMBINE model introduced from peptide inhibitors.
    Nakamura S, Nakanishi I, Kitaura K
    Bioorg Med Chem Lett16p6334-7(2006 Dec 15)
19. 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
20. 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)
21. How optimal are the binding energetics of barnase and barstar?
    Wang T, Tomic S, Gabdoulline RR, Wade RC
    Biophys J87p1618-30(2004 Sep)
22. 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.
23. 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)
24. Chemometrical identification of mutations in HIV-1 reverse transcriptase conferring resistance or enhanced sensitivity to arylsulfonylbenzonitriles.
    Rodríguez-Barrios F, Gago F
    J Am Chem Soc126p2718-9(2004 Mar 10)
25. Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors.
    Murcia M, Ortiz AR
    J Med Chem47p805-20(2004 Feb 12)
26. Modulation of binding strength in several classes of active site inhibitors of acetylcholinesterase studied by comparative binding energy analysis.
    Martín-Santamaría S, Muñoz-Muriedas J, Luque FJ, Gago F
    J Med Chem47p4471-82(2004 Aug 26)
27. 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)
28. A docking score function for estimating ligand-protein interactions: application to acetylcholinesterase inhibition.
    Guo J, Hurley MM, Wright JB, Lushington GH
    J Med Chem47p5492-500(2004 Oct 21)
29. Modeling and interactions of Aspergillus fumigatus lanosterol 14-alpha demethylase 'A' with azole antifungals.
    Gollapudy R, Ajmani S, Kulkarni SA
    Bioorg Med Chem12p2937-50(2004 Jun 1)
30. 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.
31. Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations.
    Kmunícek J, Bohác M, Luengo S, Gago F, Wade RC, Damborský J
    J Comput Aided Mol Des17p299-311(2003 May-Jun)
32. Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics.
    Wang T, Wade RC
    J Med Chem45p4828-37(2002 Oct 24)
33. A quantitative model for predicting enzyme enantioselectivity: application to Burkholderia cepacia lipase and 3-(aryloxy)-1,2-propanediol derivatives.
    Tomić S, Kojić-Prodić B
    J Mol Graph Model21p241-52(2002 Dec)
34. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes.
    Wang T, Wade RC
    J Med Chem44p961-71(2001 Mar 15)
35. 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.
36. 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.
37. 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.
38. 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)
39. Comparative binding energy (COMBINE) analysis of human neutrophil elastase inhibition by pyridone-containing trifluoromethylketones.
    Cuevas C, Pastor M, Pérez C, Gago F
    Comb Chem High Throughput Screen4p627-42(2001 Dec)
40. 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.
41. M. Pastor, F. Gago, G. Cruciani: Comparative binding energy (COMBINE) analysis on a series of glycogen phosphorylase inhibitors: comparison with GRID/GOLPE methods. 2000
42. 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)
43. 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.
44. 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).
45. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.
    Pérez C, Pastor M, Ortiz AR, Gago F
    J Med Chem41p836-52(1998 Mar 12)
46. Simulation of alternative binding modes in a structure-based QSAR study of HIV-1 protease inhibitors.
    Pastor M, Pérez C, Gago F
    J Mol Graph Model15p364-71, 389(1997 Dec)
47. Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors.
    Ortiz AR, Pastor M, Palomer A, Cruciani G, Gago F, Wade RC
    J Med Chem40p1136-48(1997 Mar 28)
48. 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)