How different are two chemical structures?

Journal of Chemical Information and Modeling

Volumn 50, Issue 12, 2010, Pages 2129-2140

  Marques, J M C ^a   Llanio Trujillo, J L ^a   Abreu, P E ^a   Pereira, F B ^b,c  

^a UNIVERSITY OF COIMBRA   (Portugal)

^b POLYTECHNIC INSTITUTE OF COIMBRA   (Portugal)

^c UNIVERSITY OF COIMBRA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

GEOMETRY; MOLECULES; STEREOCHEMISTRY;

DISCRIMINATING POWER; DISSIMILARITY MEASURES; DIVERSITY OF SOLUTIONS; GEOMETRY OPTIMIZATION; GLOBAL GEOMETRY OPTIMIZATION; MUTATION OPERATORS; ROOT-MEAN-SQUARE DISTANCES; SUPERIMPOSING METHODS;

ITERATIVE METHODS;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; CONFORMATION; STEREOISOMERISM;

ALGORITHMS; CLUSTER ANALYSIS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; STEREOISOMERISM;

EID: 78650681756     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100219f     Document Type: Article

References (51)

1. Nissink, J. W. M.; Verdonk, M. L.; Kroon, J.; Mietzner, T.; Klebe, G. Superposition of molecules: Electron density fitting by application of Fourier transforms J. Comput. Chem. 1997, 18, 638-645
2. Gironés, X.; Robert, D.; Carbó-Dorca, R. TGSA. A molecular superposition program based on topo-geometrical considerations J. Comput. Chem. 2001, 22, 255-263
3. Mestres, J.; Rohrer, D. C.; Maggiora, G. M. MIMIC: A molecular-field matching program. Exploiting applicability of molecular similarity approaches J. Comput. Chem. 1997, 18, 934-954
4. Barakat, M. T.; Dean, P. M. Molecular-structure matching by simulated annealing. 1. A comparison between different cooling schedules J. Comput.-Aided Mol. Des. 1990, 4, 295-316
5. Bayada, D. M.; Simpson, R. W.; Johnson, A. P.; Laurenço, C. An algorithm for the multiple common subgraph problem J. Chem. Inf. Comput. Sci. 1992, 32, 680-685
6. Karney, C. F. F. Quaternions in molecular modeling J. Mol. Graphics Modell. 2007, 25, 595-604
7. Flower, D. R. Rotational superposition: A review of methods J. Mol. Graphics Modell. 1999, 17, 238-244
8. Vásquez-Pérez, J. M.; Martínez, G. U. G.; Köster, A. M.; Calaminici, P. The discovery of unexpected isomers in sodium heptamers by Born-Oppenheimer molecular dynamics J. Chem. Phys. 2009, 131, 124126-1-124126-10
9. Bemis, G. W.; Kuntz, I. D. A fast and efficient method for 2D and 3D molecular shape-description J. Comput.-Aided Mol. Des. 1992, 6, 607-628
10. Nilakantan, R.; Baunman, N.; Venkataraghavan, R. New method for rapid characterization of molecular shapes-Applications in drug design J. Chem. Inf. Comput. Sci. 1993, 33, 79-85
11. Good, A. C.; Ewing, T. J. A.; Gschwend, D. A.; Kuntz, I. D. New molecular shape descriptors-Application in database screening J. Comput.-Aided Mol. Des. 1995, 9, 1-12
12. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical similarity searching J. Chem. Inf. Comput. Sci. 1998, 38, 983-996
13. Zauhar, R. J.; Moyna, G.; Tian, L. F.; Li, Z. J.; Welsh, W. J. Shape signatures: A new approach to computer-aided ligand- and receptor-based drug design J. Med. Chem. 2003, 46, 5674-5690
14. Ballester, P. J.; Richards, W. G. Ultrafast shape recognition to search compound databases for similar molecular shapes J. Comput. Chem. 2007, 28, 1711-1723
15. Grosso, A.; Locatelli, M.; Schoen, F. A population-based approach for hard global optimization problems based on dissimilarity measures Math. Program. Ser. A 2007, 110, 373-404
16. Armstrong, M. S.; Morris, G. M.; Finn, P. W.; Sharma, R.; Richards, W. G. Molecular similarity including chirality J. Mol. Graphics Modell. 2009, 28, 368-370
17. Deaven, D. M.; Ho, K. M. Molecular geometry optimization with a genetic algorithm Phys. Rev. Lett. 1995, 75, 288-291
18. n clusters using a modified genetic algorithm J. Chem. Phys. 1996, 104, 2684-2691
19. Niesse, J. A.; Mayne, H. R. Global optimization of atomic and molecular clusters using the space-fixed modified genetic algorithm method J. Comput. Chem. 1997, 18, 1233-1244
20. Roberts, C.; Johnston, R. L.; Wilson, N. T. A genetic algorithm for the structural optimization of Morse clusters Theor. Chem. Acc. 2000, 104, 123-130
21. Pereira, F. B.; Marques, J. M. C.; Leitão, T.; Tavares, J. Analysis of locality in hybrid evolutionary cluster optimization. Proceedings of the 2006 IEEE Congress on Evolutionary Computation; IEEE: New York, 2006; Vols. 1-6, pp 2270 - 2277
22. Pereira, F. B.; Marques, J. M. C.; Leitão, T.; Tavares, J. Designing efficient evolutionary algorithms for cluster optimization: A study on locality. In Advances in Metaheuristics for Hard Optimization; Springer Natural Computing Series; Siarry, P.; Michalewicz, Z., Eds.; Springer: Berlin, 2008; pp 223 - 250
23. Pereira, F. B.; Marques, J. M. C. A study on diversity for cluster geometry optimization Evol. Intel. 2009, 2, 121-140
24. Marques, J. M. C.; Pereira, F. B.; Leitão, T. On the use of different potential energy functions in rare-gas cluster optimization by genetic algorithms: Application to argon J. Phys. Chem. A 2008, 112, 6079-6089
25. Marques, J. M. C.; Pereira, F. B. An evolutionary algorithm for global minimum search of binary atomic clusters Chem. Phys. Lett. 2010, 485, 211-216
26. del Campo, J. M.; Köster, A. M. A hierarchical transition state search algorithm J. Chem. Phys. 2008, 129, 024107-1-024107-12
27. Kuhn, H. W. The Hungarian method for the assignment problem Naval Res. Logistics Quart. 1955, 2, 83-97
28. Munkres, J. Algorithms for the assignment and transportation problems J. Soc. Ind. Appl. Math. 1957, 5, 32-38
29. Code obtained from http://jblevins.org/mirror/amiller/, which is a mirror of the Fortran source code repository of Alan Miller previously located at http://users.bigpond.net.au/amiller/ (accessed June 4, 2010).
30. Kearsley, S. K. On the orthogonal transformation used for structural comparisons Acta Crystallogr., Sect. A 1989, 45, 208-210
31. Takeuchi, H. Development of an efficient geometry optimization method for water clusters J. Chem. Inf. Model. 2008, 48, 2226-2233
32. Barron, L. D. On the definition of chirality Chem. Eur. J. 1996, 2, 743-744
33. As mentioned in ref 32, Lord Kelvin stated that any geometrical figure (or group of points) has chirality if its image in a plane mirror, ideally realized, cannot be brought to coincide with itself (cf., Lord Kelvin, Baltimore Lectures, C. J. Clay, London, 1904).
34. Cahn, R. S.; Ingold, C.; Prelog, V. Specification of molecular chirality Angew. Chem., Int. Ed. 1966, 5, 385-415
35. Prelog, V.; Helmchen, G. Basic principles of the CIP-system and proposals for a revision Angew. Chem., Int. Ed. 1982, 21, 567-583
36. Schwartz, A. M.; Petitjean, M. [6.6]Chiralane: A remarkably symmetric chiral molecule Symmetry Cult. Sci. 2008, 19, 307-316
37. Marvin, 5.3.2, ChemAxon, 2010, http://www.chemaxon.com (accessed Jun 1, 2010)
38. Stewart, J. J. P. MOPAC2009, 10.153 L; Stewart Computational Chemistry: Colorado Springs, CO, 2008; http://OpenMOPAC.net (accessed Jun 1, 2010)
39. Stewart, J. J. P. Optimization of parameters for semiempirical methods I. Method J. Comput. Chem. 1989, 10, 209-220
40. Stewart, J. J. P. Optimization of parameters for semiempirical methods II. Applications J. Comput. Chem. 1989, 10, 221-264
41. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
42. Marques, J. M. C.; Pais, A. A. C. C.; Abreu, P. E. Generation and characterization of low-energy structures in atomic clusters J. Comput. Chem. 2010, 31, 1495-1503
43. Wales, D. J. Energy Landscapes: With Applications to Clusters, Biomolecules and Glasses; Cambridge University Press; Cambridge, UK, 2003
44. Ballester, P. J.; Finn, P. W.; Richards, W. G. Ultrafast shape recognition: Evaluating a new ligand-based virtual screening J. Mol. Graphics Modell. 2009, 27, 836-845
45. Ballester, P. J.; Westwood, I.; Laurieri, N.; Sim, E.; Richards, W. G. Prospective virtual screening with ultrafast shape recognition: The identification of novel inhibitors of arylamine N -acetyltransferases J. R. Soc. Interface 2010, 7, 335-342
46. Cassioli, A.; Locatelli, M.; Schoen, F. Global optimization of binary Lennard-Jones clusters Optim. Methods Software 2009, 24, 819-835
47. Aquilanti, V.; Lombardi, A.; Yurtsever, E. Global view of classical clusters: The hyperspherical approach to structure and dynamics Phys. Chem. Chem. Phys. 2002, 4, 5040-5051
48. Aquilanti, V.; Lombardi, A.; Sevryuk, M. B. Phase-space invariants for aggregates of particles: Hyperangular momenta and partitions of the classical kinetic energy J. Chem. Phys. 2004, 121, 5579-5589
49. Johnston, R. L. Evolving better nanoparticles: Genetic algorithms for optimising cluster geometries Dalton Trans. 2003, 4193-4207
50. Liu, D.; Nocedal, J. On the limited memory BFGS method for large scale optimization Math. Program. B 1989, 45, 503-528
51. Soh, H.; Ong, Y.-S.; Nguyen, Q. C.; Nguyen, Q. H.; Habibullah, M. S.; Hung, T.; Kuo, J.-L. Discovering unique, low-energy pure water isomers: Memetic exploration, optimization, and landscape analysis IEEE Trans. Evol. Comput. 2010, 14, 419-437