Emergent strategies for inverse molecular design

Science in China, Series B: Chemistry

Volumn 52, Issue 11, 2009, Pages 1769-1776

  Hu, Xiangqian ^a   Beratan, David N ^a   Yang, Weitao ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

GDMC; IBS; Inverse design; LCAP; Molecular design

Indexed keywords

INVERSE DESIGNS; MATERIAL SCIENCE; MOLECULAR DESIGN; OPTIMIZATION SCHEME; OPTIMIZATION STRATEGY;

BIOLOGY; OPTICAL DEVICES;

DESIGN;

EID: 72149088237     PISSN: 10069291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-009-0260-3     Document Type: Article

References (50)

1. H. C. Kolb M. G. Finn K. B. Sharpless 2001 Click chemistry: Diverse chemical function from a few good reactions Angew Chem, Int Ed 40 11 2004 2021 10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5 1:CAS:528:DC%2BD3MXksVOis78%3D
2. N. K. Terrett M. Gardner D. W. Gordon R. J. Kobylecki J. Steele 1995 Combinatorial synthesis - the design of compound libraries and their application to drug discovery Tetrahedron 51 30 8135 8173 10.1016/0040-4020(95)00467-M 1:CAS:528:DyaK2MXntFOrsbs%3D
3. L. A. Thompson J. A. Ellman 1996 Synthesis and applications of small molecule libraries Chem Rev 96 1 555 600 10.1021/cr9402081 1:CAS:528: DyaK28XjsVOhsA%3D%3D
4. X. D. Xiang X. D. Sun G. Briceno Y. L. Lou K. A. Wang H. Y. Chang W. G. Wallacefreedman S. W. Chen P. G. Schultz 1995 A combinatorial approach to materials discovery Science 268 5218 1738 1740 10.1126/science.268.5218.1738 1:CAS:528:DyaK2MXmsFCitr8%3D
5. R. P. Hertzberg A. J. Pope 2000 High-throughput screening: new technology for the 21st century Curr Opin Chem Biol 4 4 445 451 10.1016/S1367-5931(00) 00110-1 1:CAS:528:DC%2BD3cXlvVCisbk%3D (Pubitemid 30621048)
6. W. L. Jorgensen 2004 The many roles of computation in drug discovery Science 303 5665 1813 1818 10.1126/science.1096361 1:CAS:528: DC%2BD2cXitFehu7w%3D (Pubitemid 38374866)
7. H. van de Waterbeemd E. Gifford 2003 ADMET in silico modelling: Towards prediction paradise? Nat Rev Drug Discovery 2 3 192 204 10.1038/nrd1032 (Pubitemid 37361664)
8. T. Fink H. Bruggesser J. L. Reymond 2005 Virtual exploration of the small-molecule chemical universe below 160 daltons Angew Chem, Int Ed 44 10 1504 1508 10.1002/anie.200462457 1:CAS:528:DC%2BD2MXit12gs74%3D (Pubitemid 40460043)
9. T. Fink J. L. Reymond 2007 Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: Assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery J Chem Inf Model 47 2 342 353 10.1021/ci600423u 1:CAS:528:DC%2BD2sXhtVens7k%3D (Pubitemid 46615939)
10. W. P. Walters M. T. Stahl M. A. Murcko 1998 Virtual screening - an overview Drug Discov Today 3 4 160 178 10.1016/S1359-6446(97)01163-X 1:CAS:528:DyaK1cXisVWjur8%3D
11. M. L. Wang X. Q. Hu D. N. Beratan W. T. Yang 2006 Designing molecules by optimizing potentials J Am Chem Soc 128 10 3228 3232 10.1021/ja0572046 1:CAS:528:DC%2BD28XhsVOmtLw%3D
12. R. Das D. Baker 2008 Macromolecular modeling with Rosetta Annu Rev Biochem 77 363 382 10.1146/annurev.biochem.77.062906.171838 1:CAS:528: DC%2BD1cXos1ekurw%3D
13. A. Franceschetti A. Zunger 1999 The inverse hand-structure problem of finding an atomic configuration with given electronic properties Nature 402 6757 60 63 10.1038/46995 1:CAS:528:DyaK1MXntlCgu7c%3D (Pubitemid 29533512)
14. P. Ertl 2003 Cheminformatics analysis of organic substituents: identification of the most common substituents, calculation of substituent properties, and automatic identification of drug-like bioisosteric groups J Chem Inf Comp Sci 43 2 374 380 1:CAS:528:DC%2BD38Xpt1Cmtbs%3D
15. C. Lipinski A. Hopkins 2004 Navigating chemical space for biology and medicine Nature 432 7019 855 861 10.1038/nature03193 1:CAS:528: DC%2BD2cXhtVOht7jO (Pubitemid 40037141)
16. X. Q. Hu D. N. Beratan W. T. Yang 2008 A gradient-directed Monte Carlo approach to molecular design J Chem Phys 129 6 064102 064111 10.1063/1.2958255
17. P. Piquini P. A. Graf A. Zunger 2008 Band-gap design of quaternary (In,Ga)(As,Sb) semiconductors via the inverse-band-structure approach Phys Rev Lett 100 18 186403 186407 10.1103/PhysRevLett.100.186403 (Pubitemid 351654647)
18. G. Trimarchi A. Zunger 2008 Finding the lowest-energy crystal structure starting from randomly selected lattice vectors and atomic positions: first-principles evolutionary study of the Au-Pd, Cd-Pt, Al-Sc, Cu-Pd, Pd-Ti, and Ir-N binary systems J Phys: Condens Matter 20 29 295212 295223 10.1088/0953-8984/20/29/295212
19. D. B. Gordon S. L. Mayo 1999 Branch-and terminate: a combinatorial optimization algorithm for protein design Struct Fold Des 7 9 1089 1098 10.1016/S0969-2126(99)80176-2 1:CAS:528:DyaK1MXmtlartLs%3D (Pubitemid 29436506)
20. J. Pearl R. E. Korf 1987 Search techniques Annu Rev Comput Sci 2 451 467 10.1146/annurev.cs.02.060187.002315
21. Goldberg D E. Genetic Algorithms in Search, Optimization, and Machine Learning. New York: Addison-Wesley, 1989
22. D. Balamurugan W. T. Yang D. N. Beratan 2008 Exploring chemical space with discrete, gradient, and hybrid optimization methods J Chem Phys 129 17 174105 174114 10.1063/1.2987711 1:STN:280:DC%2BD1cjnsl2jtQ%3D%3D
23. M. Congreve R. Carr C. Murray H. Jhoti 2003 A rule of three for fragment-based lead discovery? Drug Discov Today 8 19 876 877 10.1016/S1359-6446(03)02831-9 (Pubitemid 37194496)
24. P. J. Hajduk J. Greer 2007 A decade of fragment-based drug design: strategic advances and lessons learned Nat Rev Drug Discovery 6 3 211 219 10.1038/nrd2220 1:CAS:528:DC%2BD2sXit12rtr4%3D (Pubitemid 46344625)
25. G. Schneider M.L. Lee M. Stahl P. Schneider 2000 De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks J Comput-Aided Mol Des 14 5 487 494 10.1023/A:1008184403558 1:CAS:528:DC%2BD3cXktl2ju7c%3D (Pubitemid 30386823)
26. S. Park Y. Xi J. G. Saven 2004 Advances in computational protein design Curr Opin Struct Biol 14 4 487 494 10.1016/j.sbi.2004.06.002 1:CAS:528:DC%2BD2cXmslOntL0%3D (Pubitemid 39099287)
27. R. Bonneau D. Baker 2001 Ab initio protein structure prediction: Progress and prospects Annu Rev Biophys Biomol Struct 30 173 189 10.1146/annurev. biophys.30.1.173 1:CAS:528:DC%2BD3MXkvVaqsbg%3D (Pubitemid 32566161)
28. G. Jones P. Willett R. C. Glen A. R. Leach R. Taylor 1997 Development and validation of a genetic algorithm for flexible docking J Mol Biol 267 3 727 748 10.1006/jmbi.1996.0897 1:CAS:528:DyaK2sXis1KntLo%3D (Pubitemid 27170693)
29. N. Chakraborti 2004 Genetic algorithms in materials design and processing Int Mater Rev 49 3-4 246 260 10.1179/095066004225021909 1:CAS:528: DC%2BD2cXnvFOqtr8%3D
30. S. V. Dudiy A. Zunger 2006 Searching for alloy configurations with target physical properties: Impurity design via a genetic algorithm inverse band structure approach Phys Rev Lett 97 4 046401 046405 10.1103/PhysRevLett.97. 046401 1:STN:280:DC%2BD28vosFWmtQ%3D%3D (Pubitemid 44118064)
31. M. d'Avezac A. Zunger 2007 Finding the atomic configuration with a required physical property in multi-atom structures J Phys: Condens Matter 19 40 402201 402208 10.1088/0953-8984/19/40/402201 (Pubitemid 47457961)
32. M. d'Avezac A. Zunger 2008 Identifying the minimum-energy atomic configuration on a lattice: Lamarckian twist on Darwinian evolution Phys Rev B 78 6 064102 064117 10.1103/PhysRevB.78.064102
33. P. Piquini A. Zunger 2008 Using superlattice ordering to reduce the band gap of random (In,Ga)As/InP alloys to a target value via the inverse band structure approach Phys Rev B 78 16 161302 161306 10.1103/PhysRevB.78.161302
34. S. R. Marder D. N. Beratan L. T. Cheng 1991 Approaches for optimizing the 1st electronic hyerpolarizability of conjugated organic molecules Science 252 5002 103 106 10.1126/science.252.5002.103 1:CAS:528:DyaK3MXitlylt7g%3D
35. S. M. Risser D. N. Beratan S. R. Marder 1993 Structure-function- relationships for beta, the 1st molecular hyperpolarizability J Am Chem Soc 115 17 7719 7728 10.1021/ja00070a016 1:CAS:528:DyaK3sXltFKksLc%3D
36. C. Kuhn D.N. Beratan 1996 Inverse strategies for molecular design J Phys Chem 100 25 10595 10599 10.1021/jp960518i 1:CAS:528:DyaK28Xjt1Whu7w%3D
37. W. T. Yang P. W. Ayers Q. Wu 2004 Potential functionals: Dual to density functionals and solution to the upsilon-representability problem Phys Rev Lett 92 14 146404 146408 10.1103/PhysRevLett.92.146404
38. W. T. Yang Q. Wu 2002 Direct method for optimized effective potentials in density-functional theory Phys Rev Lett 89 14 143002 143006 10.1103/PhysRevLett.89.143002
39. Q. Wu W. T. Yang 2003 A direct optimization method for calculating density functionals and exchange-correlation potentials from electron densities J Chem Phys 118 6 2498 2509 10.1063/1.1535422 1:CAS:528:DC%2BD3sXmsVWgsQ%3D%3D
40. D. Q. Xiao W. T. Yang D. N. Beratan 2008 Inverse molecular design in a tight-binding framework J Chem Phys 129 4 044106 044114 10.1063/1.2955756
41. S. Keinan X. Q. Hu D. N. Beratan W. T. Yang 2007 Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework J Phys Chem A 111 1 176 181 10.1021/jp0646168 1:CAS:528:DC%2BD28XhtlSgs73F (Pubitemid 46277961)
42. Hu X, Beratan D N, Yang W. Gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding. J Chem Phys, 2009, in press
43. Hu X, Hu H, Beratan D N, Yang W. A gradient-directed Monte Carlo approach for protein design. J Comp Chem, 2009, submitted
44. K. F. Lau K. A. Dill 1989 A lattice statistical mechanics model of the confromational and sequence spaces of proteins Macomolecules 22 10 3986 3997 10.1021/ma00200a030 1:CAS:528:DyaL1MXlslCqurY%3D
45. H. S. Chan K. A. Dill 1991 "Sequence space soup" of proteins and copolymers J Chem Phys 95 5 3775 3787 10.1063/1.460828 1:CAS:528: DyaK3MXmt1Oks7w%3D
46. K. A. Dill S. Bromberg K. Yue K. M. Fiebig D. P. Yee P. D. Thomas H. S. Chan 1995 Principles of protein folding - A perspective from simple exact models Protein Sci 4 4 561 602 1:CAS:528:DyaK2MXltFynur0%3D
47. S. K. Koh G. K. Ananthasuresh 2005 A deterministic optimization approach to protein sequence design using continuous models Int J Rob Research 24 2-3 109 130 10.1177/0278364905050354 (Pubitemid 40207001)
48. S. K. Koh G. K. Ananthasuresh C. Croke 2005 A quadratic programming formulation for the design of reduced protein models in continuous sequence space J Mech Design 127 4 728 735 10.1115/1.1901705 (Pubitemid 41064229)
49. Lesh N, Mitzenmacher M, Whitesides S. A complete and effective move set for simplied protein folding. Annual Conference on Research in Computational Molecular Biology, 2003. 188-195
50. B. Kuhlman G. Dantas G. C. Ireton G. Varani B. L. Stoddard D. Baker 2003 Design of a novel globular protein fold with atomic-level accuracy Science 302 5649 1364 1368 10.1126/science.1089427 1:CAS:528:DC%2BD3sXptVCqu7o%3D (Pubitemid 37452172)