A novel, customizable and optimizable parameter method using spherical harmonics for molecular shape similarity comparisons

Journal of Molecular Modeling

Volumn 18, Issue 4, 2012, Pages 1597-1610

  Cai, Chaoqian ^a   Gong, Jiayu ^a   Liu, Xiaofeng ^b   Jiang, Hualiang ^b   Gao, Daqi ^a   Li, Honglin ^b  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Genetic optimization; Molecular shape; Similarity comparison; Spherical harmonic; Virtual screening

Indexed keywords

ANALYTIC METHOD; ARTICLE; GENETIC ALGORITHM; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; PARTICLE SIZE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SPHERICAL HARMONIC EXPANSION BASED MOLECULAR SIMILARITY METHOD; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING; VIRTUAL REALITY;

CHOLINESTERASES; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; PROTEINS;

EID: 84861234741     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1173-6     Document Type: Article

References (50)

1. Rester U (2008) From virtuality to reality - Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective. Curr Opin Drug Discov Dev 11:559-568 (Pubitemid 351950850)
2. Shoichet BK (2004) Virtual screening of chemical libraries. Nature 432:862-865 (Pubitemid 40037142)
3. Kirchmair J, Markt P, Distinto S, Schuster D, Spitzer GM, Liedl KR, Langer T, Wolber G (2008) The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery. J Med Chem 51:7021-7040
4. Hristozov DP, Oprea TI, Gasteiger J (2007) Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios. J Comput Aided Mol Des 21:617-640 (Pubitemid 50003623)
5. Waszkowycz B (2008) Towards improving compound selection in structure-based virtual screening. Drug Discov Today 13:219-226
6. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3:935-949 (Pubitemid 39529931)
7. Lengauer T, Rarey M (1996) Computational methods for biomolecular docking. Curr Opin Struct Biol 6:402-406 (Pubitemid 26197442)
8. Evers A, Hessler G, Matter H, Klabunde T (2005) Virtual screening of biogenic amine-binding G-protein coupled receptors: Comparative evaluation of protein- and ligand-based virtual screening protocols. J Med Chem 48:5448-5465 (Pubitemid 41209243)
9. Hawkins PCD, Skillman AG, Nicholls A (2007) Comparison of shape-matching and docking as virtual screening tools. J Med Chem 50:74-82 (Pubitemid 46105500)
10. McGaughey GB, Sheridan RP, Bayly CI, Culberson JC, Kreatsoulas C, Lindsley S, Maiorov V, Truchon JF, Cornell WD (2007) Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 47:1504-1519 (Pubitemid 47210053)
11. Perez-Nueno VI, Ritchie DW, Rabal O, Pascual R, Borrell JI, Teixido J (2008) Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligandreceptor docking. J Chem Inf Model 48:509-533 (Pubitemid 351535420)
12. Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49:5912-5931 (Pubitemid 44484938)
13. Tirado-Rives J, Jorgensen WL (2006) Contribution of conformer focusing to the uncertainty in predicting free energies for proteinligand binding. J Med Chem 49:5880-5884 (Pubitemid 44484934)
14. Gohlke H, Klebe G (2002) Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew Chem Int Ed Engl 41:2645-2676
15. Daylight Chemical Information Systems, Inc. Daylight Chemical Information Systems Inc. http://www.daylight.com. Accessed 1 May 2010
16. Tripos, Inc. http://www.tripos.com. Accessed 1 May 2010
17. Durant JL, Leland BA, Henry DR, Nourse JG (2002) Reoptimization of MDL keys for use in drug discovery. J Chem Inf Comput Sci 42:1273-1280 (Pubitemid 35468313)
18. Cheeseright TJ, Mackey MD, Melville JL, Vinter JG (2008) FieldScreen: Virtual Screening Using Molecular Fields. Application to the DUD Data Set. J Chem Inf Model 48:2108-2117
19. Cheeseright T, Mackey M, Rose S, Vinter A (2006) Molecular field extrema as descriptors of biological activity: definition and validation. J Chem Inf Model 46:665-676
20. Marin RM, Aguirre NF, Daza EE (2008) Graph theoretical similarity approach to compare molecular electrostatic potentials. J Chem Inf Model 48:109-118 (Pubitemid 351271055)
21. Ronkko T, Tervo AJ, Parkkinen J, Poso A (2006) BRUTUS: optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization. J Comput Aided Mol Des 20:227-236 (Pubitemid 44317515)
22. Thorner DA, Willett P, Wright PM, Taylor R (1997) Similarity searching in files of three-dimensional chemical structures: representation and searching of molecular electrostatic potentials using field-graphs. J Comput Aided Mol Des 11:163-174 (Pubitemid 127508827)
23. Vainio MJ, Puranen JS, Johnson MS (2009) ShaEP: molecular overlay based on shape and electrostatic potential. J Chem Inf Model 49:492-502
24. Good AC, Hodgkin EE, Richards WG (1992) The utilisation of Gaussian functions for the rapid evaluation of molecular similarity. J Comput Inf Comput Sci 32:188-191
25. Grant JA, Gallardo MA, Pickup BT (1996) A fast method of molecular shape comparison: a simple application of Gaussian descriptor of molecular shape. J Comput Chem 17:1653-1666 (Pubitemid 126535414)
26. Ballester PJ, Richards WG (2007) Ultrafast shape recognition to search compound databases for similar molecular shapes. J Comput Chem 28:1711-1723 (Pubitemid 47146547)
27. Ballester PJ, Finn PW, Richards WG (2009) Ultrafast shape recognition: evaluating a new ligand-based virtual screening technology. J Mol Graph Model 27:836-845
28. Ballester PJ (2011) Ultrafast shape recognition: method and applications. Future Med Chem 3:65-78
29. Mavridis L, Hudson BD, Ritchie DW (2007) Toward high throughput 3D virtual screening using spherical harmonic surface representations. J Chem Inf Model 47:1787-1796 (Pubitemid 47561126)
30. Cai WS, Shao XG, Maigret B (2002) Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening. J Mol Graph Model 20:313-328 (Pubitemid 34019229)
31. Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 21:2347-2355 (Pubitemid 40731589)
32. Jakobi AJ, Mauser H, Clark T (2008) ParaFrag-an approach for surface-based similarity comparison of molecular fragments. J Mol Model 14:547-558
33. DiMaio FP, Soni AB, Phillips GN, Shavlik JW (2009) Sphericalharmonic decomposition for molecular recognition in electrondensity maps. Int J Data Min Bioinform 3:205-227
34. Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49:6789-6801 (Pubitemid 44749746)
35. A directory of useful decoys. http://dud.docking.org/. Accessed 13 June 2010
36. Jahn A, Hinselmann G, Fechner N, Zell A (2009) Optimal assignment methods for ligand-based virtual screening. J Cheminform 1:14
37. Good AC, Oprea TI (2008) Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J Comput Aided Mol Des 22:169-178
38. Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50:742-754
39. Accelrys, Inc. http://accelrys.com/. Accessed 1 May 2010
40. Ritchie DW, Kemp GJL (1999) Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J Comput Chem 20:383-395 (Pubitemid 129652338)
41. Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221(4612):709-713
42. Laurikkala J (2001) Improving identification of difficult small classes by balancing class distribution. Lecture Notes Comput Sci 2101:63-66 (Pubitemid 33301585)
43. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21:4663-4670 (Pubitemid 34984353)
44. Nicholls A (2008) What do we know and when do we know it? J Comput Aided Mol Des 22:239-255
45. Truchon JF, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J Chem Inf Model 47:488-508 (Pubitemid 46615951)
46. Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B (2010) Molecular shape and medicinal chemistry: a perspective. J Med Chem 53:3862-3886
47. Kahraman A, Morris RJ, Laskowski RA, Thornton JM (2007) Shape variation in protein binding pockets and their ligands. J Mol Biol 368:283-301 (Pubitemid 46454307)
48. Kirchmair J, Markt P, Distinto S, Wolber G, Langer T (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection- what can we learn from earlier mistakes? J Comput Aided Mol Des 22:213-228 (Pubitemid 351447959)
49. Jain AN, Nicholls A (2008) Recommendations for evaluation of computational methods. J Comput Aided Mol Des 22:133-139
50. Irwin JJ, Shoichet BK (2005) ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 45:177-182 (Pubitemid 40736970)