MolShaCS: A free and open source tool for ligand similarity identification based on Gaussian descriptors

European Journal of Medicinal Chemistry

Volumn 59, Issue , 2013, Pages 296-303

  Vaz De Lima, Luis Antônio C ^a   Nascimento, Alessandro S ^a,b  

^a UNIVERSIDADE FEDERAL DO ABC   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Gaussian descriptors; Molecular similarity; MolShaCS

Indexed keywords

ALDOSTERONE; LIGAND; MINERALOCORTICOID RECEPTOR;

ARTICLE; CHEMICAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR SIMILARITY; NORMAL DISTRIBUTION; SURFACE CHARGE;

COMPUTER SIMULATION; LIGANDS; MODELS, MOLECULAR; NORMAL DISTRIBUTION; SOFTWARE;

EID: 84870662439     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2012.11.013     Document Type: Article

References (48)

1. A. Bender, and R.C. Glen Molecular similarity: a key technique in molecular informatics Org. Biomol. Chem. 2 2004 3204 3218
2. D.E. Patterson, R.D. Cramer, A.M. Ferguson, R.D. Clark, and L.E. Weinberger Neighborhood behavior: a useful concept for validation of 'molecular diversity' descriptors J. Med. Chem. 39 1996 3049 3059
3. H. Eckert, and J. Bojorath Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches Drug Discov. Today 12 2007 225 233
4. A.J. McMahon, and P.M. King Optimization of Carbo molecular similarity index using gradient methods J. Comput. Chem. 18 1997 151 158
5. Daylight Fingerprints, Version 4.62 1999 Daylight Chemical Information Systems Laguna Niguel, CA
6. MACCS Structural Keys 2010 Symyx Software San Ramon, CA
7. M.J. Keiser, B.L. Roth, B.N. Armbruster, P. Ernsberger, J.J. Irwin, and B.K. Shoichet Relating protein pharmacology by ligand chemistry Nat. Biotechnol. 25 2007 197 206
8. X. Liu, H. Jiang, and H. Li SHAFTS: a hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening J. Chem. Inf. Model. 51 2011 2372 2385
9. M.S. Armstrong, G.M. Morris, P.W. Finn, R. Sharma, L. Moretti, R.I. Cooper, and W.G. Richards ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics J. Comput. Aided Mol. Des. 24 2010 789 801
10. M.J. Vainio, J.S. Puranen, and M.S. Johnson ShaEP: molecular overlay based on shape and electrostatic potential J. Chem. Inf. Model. 49 2009 492 502
11. ROCS 2012 OpenEye Scientific Software Santa Fe, NM
12. J.A. Grant, M.A. Gallardo, and B.T. Pickup A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape J. Comput. Chem. 17 1996 1653 1666
13. J.A. Grant, and B.T. Pickup A Gaussian description of molecular shape J. Phys. Chem. 99 1995 3503 3510
14. I. Muegge, and I. Enyedy Virtual screening Burger's Medicinal Chemistry and Drug Discovery 2003 John Wiley & Sons, Inc.
15. P.W. Kenny Hydrogen bonding, electrostatic potential, and molecular design J. Chem. Inf. Model. 49 2009 1234 1244
16. P. Bultinck Computational Medicinal Chemistry for Drug Discovery 2004 Marcel Dekker New York
17. P.v.R. Schleyer Encyclopedia of Computational Chemistry 1998 John Wiley Chichester, New York
18. J.B. Brown, and Y. Okuno Systems biology and systems chemistry: new directions for drug discovery Chem. Biol. 19 2012 23 28
19. J. von Eichborn, M.S. Murgueitio, M. Dunkel, S. Koerner, P.E. Bourne, and R. Preissner PROMISCUOUS: a database for network-based drug-repositioning Nucleic Acids Res. 39 2011 D1060 D1066
20. L. Yang, K. Wang, J. Chen, A.G. Jegga, H. Luo, L. Shi, C. Wan, X. Guo, S. Qin, G. He, G. Feng, and L. He Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome-clozapine-induced agranulocytosis as a case study PLoS Comput. Biol. 7 2011 e1002016
21. N.P. Tatonetti, T.Y. Liu, and R.B. Altman Predicting drug side-effects by chemical systems biology Genome Biol. 10 2009
22. J. Scheiber, B. Chen, M. Milik, S.C.K. Sukuru, A. Bender, D. Mikhailov, S. Whitebread, J. Hamon, K. Azzaoui, L. Urban, M. Glick, J.W. Davies, and J.L. Jenkins Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis J. Chem. Inf. Model. 49 2009 308 317
23. A. Flemming Chemoinformatics: where 'magic bullets' go astray Nat. Rev. Drug Discov. 8 2009 933
24. E.G. Birgin, and J.M. Martinez Improving ultimate convergence of an augmented Lagrangian method Optim. Methods Softw. 23 2008 177 195
25. R. Andreani, E.G. Birgin, J.M. Martinez, and M.L. Schuverdt On augmented Lagrangian methods with general lower-level constraints SIAM J. Optim. 18 2007 1286 1309
26. R. Andreani, E.G. Birgin, J.M. Martinez, and M.L. Schuverdt Augmented Lagrangian methods under the constant positive linear dependence constraint qualification Math. Program. 111 2008 5 32
27. A. Jahn, G. Hinselmann, N. Fechner, and A. Zell Optimal assignment methods for ligand-based virtual screening J. Cheminform. 1 2009 14
28. J. Wang, W. Wang, P.A. Kollman, and D.A. Case Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graph. Model. 25 2006 247 260
29. M.S. Armstrong, P.W. Finn, G.M. Morris, and W.G. Richards Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension J. Comput. Aided Mol. Des. 25 2011 785 790
30. N.M. O'Boyle, M. Banck, C.A. James, C. Morley, T. Vandermeersch, and G.R. Hutchison Open Babel: an open chemical toolbox J. Cheminform. 3 2011 33
31. M.A. Miteva, F. Guyon, and P. Tuffery Frog2: efficient 3D conformation ensemble generator for small compounds Nucleic Acids Res. 38 2010 W622 W627
32. J.L. Arriza, C. Weinberger, G. Cerelli, T.M. Glaser, B.L. Handelin, D.E. Housman, and R.M. Evans Cloning of human mineralocorticoid receptor complementary DNA: structural and functional kinship with the glucocorticoid receptor Science 237 1987 268 275
33. C. Grossmann, T. Scholz, M. Rochel, C. Bumke-Vogt, W. Oelkers, A.F. Pfeiffer, S. Diederich, and V. Bahr Transactivation via the human glucocorticoid and mineralocorticoid receptor by therapeutically used steroids in CV-1 cells: a comparison of their glucocorticoid and mineralocorticoid properties Eur. J. Endocrinol. 151 2004 397 406
34. J.J. Irwin, and B.K. Shoichet ZINC a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182
35. A.J. Rickard, J.W. Funder, P.J. Fuller, and M.J. Young The role of the glucocorticoid receptor in mineralocorticoid/salt-mediated cardiac fibrosis Endocrinology 147 2006 5901 5906
36. L.A. Druce, C.M. Thorpe, and A. Wilton Mineralocorticoid effects due to cortisol inactivation overload explain the beneficial use of hydrocortisone in septic shock Med. Hypotheses 70 2008 56 60
37. M.E. Rafestin-Oblin, A. Souque, B. Bocchi, G. Pinon, J. Fagart, and A. Vandewalle The severe form of hypertension caused by the activating S810L mutation in the mineralocorticoid receptor is cortisone related Endocrinology 144 2003 528 533
38. M. Bureik, N. Bruck, K. Hubel, and R. Bernhardt The human mineralocorticoid receptor only partially differentiates between different ligands after expression in fission yeast FEMS Yeast Res. 5 2005 627 633
39. P. Galuppo, and J. Bauersachs Mineralocorticoid receptor activation in myocardial infarction and failure: recent advances Eur. J. Clin. Invest. 42 2012 1112 1120
40. J. Born, A. Zwick, G. Roth, G. Fehmwolfsdorf, and H.L. Fehm Differential-effects of hydrocortisone, fluocortolone, and aldosterone on nocturnal sleep in humans Acta Endocrinol. 116 1987 129 137
41. L.V. Kulemina, and D.A. Ostrov Prediction of off-target effects on angiotensin-converting enzyme 2 J. Biomol. Screen. 16 2011 878 885
42. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case Development and testing of a general amber force field J. Comput. Chem. 25 2004 1157 1174
43. E.E. Hodgkin, and W.G. Richards Molecular similarity based on electrostatic potential and electric-field Int. J. Quantum Chem. 1987 105 110
44. A.C. Good, E.E. Hodgkin, and W.G. Richards Similarity screening of molecular-data sets J. Comput. Aided Mol. Des. 6 1992 513 520
45. K. Svanberg A class of globally convergent optimization methods based on conservative convex separable approximations SIAM J. Optim. 12 2001 555 573
46. S.G. Jhonson, The NLopt nonlinear-optimization package, in: The NLopt nonlinear-optimization package, http://ab-initio.mit.edu/nlopt.
47. N. Huang, B.K. Shoichet, and J.J. Irwin Benchmarking sets for molecular docking J. Med. Chem. 49 2006 6789 6801
48. J.J. Irwin, T. Sterling, M.M. Mysinger, E.S. Bolstad, and R.G. Coleman ZINC: a free tool to discover chemistry for biology J. Chem. Inf. Model. 2012