Chemotopology: Beyond neighbourhoods

Current Computer-Aided Drug Design

Volumn 7, Issue 2, 2011, Pages 90-97

  Restrepo, Guillermo ^a   Mesa, Héber ^b  

^a UNIVERSIDAD DE PAMPLONA   (Colombia)

^b UNIVERSIDAD DEL VALLE   (Colombia)

Author keywords

Amino acids; Benzimidazoles; Chemical elements; Chemotopology; Hydrides; Neighbourhoods; Steroids; Topology

Indexed keywords

AMINO ACIDS; CHEMICAL ELEMENTS; CLUSTER ANALYSIS; HIERARCHICAL SYSTEMS; TOPOLOGY;

AMINO-ACIDS; BENZIMIDAZOLES; CHEMOTOPOLOGY; DENDROGRAMS; HIERARCHICAL CLUSTER ANALYSIS; MATHEMATICAL CHARACTERIZATION; NEIGHBOURHOOD; PROPERTY; SETPOINTS; STEROID;

HYDRIDES;

AMINO ACID; BENZIMIDAZOLE; STEROID;

ANALYTIC METHOD; ARTICLE; CHEMICAL ANALYSIS; CLUSTER ANALYSIS; CONTROLLED STUDY; DRUG DEVELOPMENT; MATHEMATICAL ANALYSIS; PHYLOGENETIC TREE;

EID: 79956276143     PISSN: 15734099     EISSN: 18756697     Source Type: Journal    
DOI: 10.2174/157340911795677585     Document Type: Article

References (47)

1. Restrepo, G.; Mesa, H.; Llanos, E. J.; Villaveces, J.L. Topologicalstudy of the periodic system. J. Chem. Inf. Comput. Sci., 2004, 44,68-75.
2. Restrepo, G. Los elementos químicos, su matemática y relación conel sistema periódico. Bistua, 2004, 2, 91-98.
3. Restrepo, G.; Villaveces, J.L. From trees (dendrograms andconsensus trees) to topology. Croat. Chem. Acta, 2005, 78, 275-281.
4. Restrepo, G. Química matemática y la Universidad de Pamplona. Bistua, 2005, 3, 61-76.
5. Sokal, R.R.; Sneath, P.H. A. Principles of numerical taxonomy; W.H. Freeman: San Francisco, 1963.
6. Everitt, B. S. Cluster analysis; Edward Arnold: Bristol, 1993.
7. Rouvray, D.H. Definition and role of similarity concepts in thechemical and physical sciences. J. Chem. Inf. Comput. Sci., 1992,32, 580-586.
8. Johnson, M.A. A review and examination of the mathematicalspaces underlying molecular similarity analysis. J. Math. Chem.,1989, 3, 117-145.
9. Basak, S.C.; Grunwald, G.D. Tolerance space and molecularsimilarity. SAR QSAR Environ. Res., 1995, 3, 265-277.
10. Restrepo, G.; Brüggemann, R. Ranking regions through clusteranalysis and posets. WSEAS Trans. Inf. Sci. Appl., 2005, 2, 976-981.
11. Schreider, J.A. Equality, resemblance and order; Mir publishers:Moscow, 1975.
12. Restrepo, G.; Llanos, E.J.; Bernal, A. A novel method for selectingclusters in cluster analysis. In Advances in computational methodsin sciences and engineering 2005; Simos, T., Ed.; VSP: Leiden,2005; 4 A &4 B, 1582-1585.
13. Lipschutz, S. General topology; McGraw-Hill: New York, 1965.
14. Lucas, J.R. The conceptual roots of mathematics; Routledge: NewYork, 2000.
15. Basak, S.C.; Gute, B.D.; Mills, D. Quantitative molecular similarityanalysis (QMSA) methods for property estimation: a comparison ofproperty-based, arbitrary, and tailored similarity spaces. SAR QSAREnviron. Res., 2002, 13, 727-742.
16. Basak, S.C.; Gute, B.D.; Mills, D.; Hawkins, D.M. Quantitativemolecular similarity methods in the property/ toxicity estimation ofchemicals: a comparison of arbitrary versus tailored similarityspaces. J. Mol. Struct. THEOCHEM, 2003, 622, 127-145.
17. Potter, M. Set theory and its philosophy; Oxford university press:Oxford, 2004.
18. Restrepo, G.; Mesa, H.; Llanos, E.J. Three dissimilarity measuresto contrast dendrograms. J. Chem. Inf. Model., 2007, 47, 761-770.
19. Boorman, S.A.; Olivier, D.C. Metrics on spaces of finite trees. J.Math. Psych., 1973, 10, 26-59.
20. Wild, D.J.; Blankley, C.J. Comparison of 2D fingerprint types andhierarchy level selection methods for structural grouping usingWard's clustering. J. Chem. Inf. Comput. Sci., 2000, 40, 155-162.
21. Restrepo, G.; Weckert, M.; Brüggemann, R.; Gerstmann, S.; Frank, H. Refrigerants ranked by partial order theory. In: EnviroInfo 2007,21st international conference on informatics for environmentalprotection; Hryniewicz, O.; Studzin'ski, J.; Szediw, A., Eds.;Shaker: Aachen, 2007, pp. 209-217.
22. Restrepo, G.; Brüggemann, R.; Weckert, M.; Gerstmann, S.; Frank, H. Ranking patterns, an application to refrigerants. MATCHCommun. Math. Comput. Chem., 2008, 59, 555-584.
23. Restrepo, G.; Weckert, M.; Brüggemann, R.; Gerstmann, S.; Frank, H. Ranking of refrigerants. Environ. Sci. Technol., 2008, 42, 2925-2930.
24. Brüggemann, R.; Restrepo, G.; Voigt, K. Towards an evaluation ofchemicals. WSEAS Trans. Inf. Sci. Appl., 2005, 2, 1023-1033.
25. Brüggemann, R.; Restrepo, G.; Voigt, K. Structure-faterelationships of organic chemicals derived from the softwarepackages E4CHEM and WHASSE. J. Chem. Inf. Model., 2006, 46,894-902.
26. Restrepo, G.; Brüggemann, R. Partially ordered sets in the analysisof alkanes fate in rivers. Croat. Chem. Acta, 2007, 80, 261-270.
27. Restrepo, G.; Brüggemann, R. Dominance and separability inposets, their application to isoelectronic species with equal totalnuclear charge, J. Math. Chem., 2008, 44, 577-602.
28. Brüggemann, R.; Voigt, K.; Restrepo, G.; Simon, U. The conceptof stability fields and hot spots in ranking of environmentalchemicals. Environ. Model. Softw., 2008, 23, 1000-1012.
29. Brüggemann, R.; Restrepo, G.; Voigt, K. Towards a new andadvanced partial order program: Pyhasse. In: Multicriteria orderingand ranking: Partial orders, ambiguities and applied issues; Owsinski, J. W.; Brüggemann, R., Eds.; Polish Academy ofSciences: Warsaw, 2008; pp. 11-33.
30. Klein, D.J.; Rosenfeld, V.; Restrepo, G. Stereo-chemicalcombinatorics & beyond. AIP Conf. Proc., 2009, 1148, 421-424.
31. Nava, J.; Kreinovich, V.; Restrepo, G.; Klein, D. Discrete Taylorseries as a simple way to predict properties of chemical substanceslike benzenes and cubanes. J. Uncert. Syst., 2010, 4, pages to beassigned, online at:http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.156.1763
32. Restrepo, G.; Br̈ggemann, R.; Klein, D.J. Partially ordered sets:ranking and prediction of substances' properties. Curr. Comput.-Aided Drug Des., 2011, 7, 133-145.
33. Schummer, J. The chemical core of chemistry I: a conceptualapproach. HYLE, 1998, 4-2, 129-162.
34. Restrepo, G.; Mesa, H.; Llanos, E.J.; Villaveces, J.L. Topologicalstudy of the periodic system. In: The mathematics of the periodictable; King, R. B.; Rouvray, D. H., Eds.; Nova: New York, 2006;pp. 75-100.
35. Restrepo, G.; Mesa, H.; Villaveces, J.L. On the topological sense ofchemical sets. J. Math. Chem., 2006, 39, 363-376.
36. Rayner-Canham, G. Periodic patterns. J. Chem. Educ., 2000, 77,1053-1056.
37. Restrepo, G.; Llanos, E.J.; Mesa, H. Topological space of thechemical elements and its properties. J. Math. Chem., 2006, 39,401-416.
38. Restrepo, G.; Pachón, L. Mathematical aspects of the periodic law.Found. Chem., 2007, 9, 189-214.
39. Leal, W.; Restrepo, G. Chemical elements, their sociology. J. Sci.Educ., 2009, 10, 126-127.
40. Leal, W.; Bernal, A.; Restrepo, G. Binary compounds, atopological study. In preparation.
41. Niño, M.; Daza, E.E.; Tello, M. A criteria to classify biologicalactivity of benzimidazoles from a model of structural similarity. J.Chem. Inf. Comput. Sci., 2001, 41, 495-504.
42. Bultinck, P.; Carbó-Dorca, R. Molecular quantum similarity matrixbased clustering of molecules using dendrograms. J. Chem. Inf.Comput. Sci., 2003, 43, 170-177.
43. Cárdenas, C.; Obregón, M.; Llanos, E.J.; Machado, E.; Bohórquez, H.J.; Villaveces, J.L.; Patarroyo, M.E. Constructing a useful toolfor characterizing amino acid conformers by means of quantumchemical and graph theory indices. Comput. Chem., 2002, 26, 667-682.
44. Nelson, D.L.; Lehninger, A.L.; Cox, M.M. Lehninger principles ofbiochemistry; W.H. Freeman: New York, 2000.
45. Uribe, E.A.; Daza, M.C.; Restrepo, G. Chemotopological study ofthe fourth period mono-hydrides. WSEAS Trans. Inf. Sci. Appl.,2005, 2, 1085-1090.
46. Daza, M.C.; Restrepo, G.; Uribe, E.A.; Villaveces, J.L. Quantumchemical and chemotopological study of fourth row monohydrides. Chem. Phys. Lett., 2006, 428, 55-61.
47. Mesa, H.; Restrepo, G. On dendrograms and topologies. MATCH Commun. Math. Comput., 2008, 60, 371-384.