메뉴 건너뛰기




Volumn 50, Issue 9, 2010, Pages 1644-1659

GARLig: A fully automated tool for subset selection of large fragment spaces via a self-adaptive genetic algorithm

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOCHIPS; ENZYMES; LIBRARIES; REAGENTS; SCAFFOLDS; SOFTWARE TESTING; SUBSTRATES;

EID: 77957227802     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9003305     Document Type: Article
Times cited : (13)

References (58)
  • 1
    • 23844449940 scopus 로고    scopus 로고
    • Computer-based de novo design of drug-like molecules
    • DOI 10.1038/nrd1799
    • Schneider, G.; Fechner, U. Computer-based de novo design of drug-like molecules Nat. Rev. Drug Discovery 2005, 4, 649-63 (Pubitemid 41149759)
    • (2005) Nature Reviews Drug Discovery , vol.4 , Issue.8 , pp. 649-663
    • Schneider, G.1    Fechner, U.2
  • 2
    • 0028380643 scopus 로고
    • CAVEAT: A program to facilitate the design of organic molecules
    • Lauri, G.; Bartlett, P. CAVEAT: A program to facilitate the design of organic molecules J. Comput.-Aided Mol. Des. 1994, 8, 51-66
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 51-66
    • Lauri, G.1    Bartlett, P.2
  • 4
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Böhm, H. J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors J. Comput.-Aided Mol. Des. 1992, 6, 61-78
    • (1992) J. Comput.-Aided Mol. Des. , vol.6 , pp. 61-78
    • Böhm, H.J.1
  • 6
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • DOI 10.1023/A:1011115820450
    • Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases J. Comput.-Aided Mol. Des. 2001, 15, 411-28 (Pubitemid 32452109)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.5 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 7
    • 0040541621 scopus 로고    scopus 로고
    • Combinatorial docking and combinatorial chemistry: Design of potent non- peptide thrombin inhibitors
    • DOI 10.1023/A:1008040531766
    • Böhm, H.-J.; Banner, D.; Weber, L. Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors J. Comput.-Aided Mol. Des. 1999, 1, 51-56 (Pubitemid 29098942)
    • (1999) Journal of Computer-Aided Molecular Design , vol.13 , Issue.1 , pp. 51-56
    • Bohm, H.-J.1    Banner, D.W.2    Weber, L.3
  • 8
    • 33947585518 scopus 로고    scopus 로고
    • Ultrafast de novo docking combining pharmacophores and combinatorics
    • DOI 10.1007/s10822-006-9091-x, Advances in Phatmacophores and 3-D Screening
    • Gastreich, M.; Lilienthal, M.; Briem, H.; Claussen, H. Ultrafast de novo docking combining pharmacophores and combinatorics. J. Comput.-Aided Mol. Des. 2007, 12, 717-734. (Pubitemid 46476942)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.12 , pp. 717-734
    • Gastreich, M.1    Lilienthal, M.2    Briem, H.3    Claussen, H.4
  • 9
    • 33748652464 scopus 로고    scopus 로고
    • FLEXNOVO: Structure-based searching in large fragment spaces
    • DOI 10.1002/cmdc.200500102
    • Degen, J.; Rarey, M. FlexNovo: Structure-based searching in large fragment spaces ChemMedChem 2006, 1, 854-68 (Pubitemid 44384546)
    • (2006) ChemMedChem , vol.1 , Issue.8 , pp. 854-868
    • Degen, J.1    Rarey, M.2
  • 10
    • 36848998994 scopus 로고    scopus 로고
    • KNOBLE: A knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding
    • DOI 10.1002/anie.200703323
    • Gerlach, C.; Munzel, M.; Baum, B.; Gerber, H. D.; Craan, T.; Diederich, W. E.; Klebe, G. KNOBLE: A knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding Angew. Chem., Int. Ed. Engl. 2007, 46, 9105-9 (Pubitemid 350232778)
    • (2007) Angewandte Chemie - International Edition , vol.46 , Issue.47 , pp. 9105-9109
    • Gerlach, C.1    Munzel, M.2    Baum, B.3    Gerber, H.-D.4    Craan, T.5    Diederich, W.E.6    Klebe, G.7
  • 11
    • 33744935012 scopus 로고    scopus 로고
    • From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
    • DOI 10.1016/j.jmb.2006.04.024, PII S0022283606004724
    • Kuhn, D.; Weskamp, N.; Schmitt, S.; Hüllermeier, E.; Klebe, G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase J. Mol. Biol. 2006, 359, 1023-44 (Pubitemid 43842050)
    • (2006) Journal of Molecular Biology , vol.359 , Issue.4 , pp. 1023-1044
    • Kuhn, D.1    Weskamp, N.2    Schmitt, S.3    Hullermeier, E.4    Klebe, G.5
  • 13
    • 33746891508 scopus 로고    scopus 로고
    • GLARE: A New Approach for Filtering Large Reagent Lists in Combinatorial Library Design Using Product Properties
    • 4, 1536-48
    • Truchon, J. F.; Bayly, C. I. GLARE: A New Approach for Filtering Large Reagent Lists in Combinatorial Library Design Using Product Properties. J. Chem. Inf. Model. 2006, 4, 1536-48.
    • (2006) J. Chem. Inf. Model.
    • Truchon, J.F.1    Bayly, C.I.2
  • 14
    • 0000340904 scopus 로고    scopus 로고
    • Ultrafast algorithm for designing focused combinational arrays
    • Agrafiotis, D. K.; Lobanov, V. S. Ultrafast algorithm for designing focused combinational arrays J. Chem. Inf. Comput. Sci. 2000, 40, 1030-8
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 1030-1038
    • Agrafiotis, D.K.1    Lobanov, V.S.2
  • 16
    • 0032587975 scopus 로고    scopus 로고
    • Rational combinatorial library design. 3. Simulated annealing guided evaluation (SAGE) of molecular diversity: A novel computational tool for universal library design and database mining
    • Zheng, W.; Cho, S. J.; Waller, C. L.; Tropsha, A. Rational combinatorial library design. 3. Simulated annealing guided evaluation (SAGE) of molecular diversity: a novel computational tool for universal library design and database mining J. Chem. Inf. Comput. Sci. 1999, 39, 738-46
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 738-746
    • Zheng, W.1    Cho, S.J.2    Waller, C.L.3    Tropsha, A.4
  • 17
    • 0030831365 scopus 로고    scopus 로고
    • New Methodology for Profiling Combinatorial Libraries and Screening Sets: Cleaning Up the Design Process with HARPick
    • Good, A. C.; Lewis, R. A. New Methodology for Profiling Combinatorial Libraries and Screening Sets: Cleaning Up the Design Process with HARPick J. Med. Chem. 1997, 40, 3926-3936
    • (1997) J. Med. Chem. , vol.40 , pp. 3926-3936
    • Good, A.C.1    Lewis, R.A.2
  • 18
  • 19
    • 0032011973 scopus 로고    scopus 로고
    • Rational combinatorial library design. 1. Focus-2D: A new approach to the design of targeted combinatorial chemical libraries
    • Zheng, W.; Cho, S. J.; Tropsha, A. Rational combinatorial library design. 1. Focus-2D: A new approach to the design of targeted combinatorial chemical libraries J. Chem. Inf. Model. 1998, 38, 251-258 (Pubitemid 128591242)
    • (1998) Journal of Chemical Information and Computer Sciences , vol.38 , Issue.2 , pp. 251-258
    • Zheng, W.1    Cho, S.J.2    Tropsha, A.3
  • 20
    • 0033654770 scopus 로고    scopus 로고
    • PICCOLO: A tool for combinatorial library design via multicriterion optimization
    • Zheng, W.; Hung, S. T.; Saunders, J. T.; Seibel, G. L. PICCOLO: a tool for combinatorial library design via multicriterion optimization Pac. Symp. Biocomput. 2000, 588-599
    • (2000) Pac. Symp. Biocomput. , pp. 588-599
    • Zheng, W.1    Hung, S.T.2    Saunders, J.T.3    Seibel, G.L.4
  • 21
    • 0034130399 scopus 로고    scopus 로고
    • De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
    • DOI 10.1023/A:1008184403558
    • Schneider, G.; Lee, M.-L.; Stahl, M.; Schneider, P. De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks J. Comput.-Aided Mol. Des. 2000, 14, 487-494 (Pubitemid 30386823)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.5 , pp. 487-494
    • Schneider, G.1    Lee, M.-L.2    Stahl, M.3    Schneider, P.4
  • 22
    • 33646265985 scopus 로고    scopus 로고
    • Flux (1): A virtual synthesis scheme for fragment-based de novo design
    • Fechner, U.; Schneider, G. Flux (1): A virtual synthesis scheme for fragment-based de novo design J. Chem. Inf. Model. 2006, 46, 699-707
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 699-707
    • Fechner, U.1    Schneider, G.2
  • 23
    • 49449112269 scopus 로고    scopus 로고
    • Identification of hits and lead structure candidates with limited resources by adaptive optimization
    • Schuller, A.; Schneider, G. Identification of hits and lead structure candidates with limited resources by adaptive optimization J. Chem. Inf. Model. 2008, 48, 1473-91
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1473-1491
    • Schuller, A.1    Schneider, G.2
  • 25
    • 0030815955 scopus 로고    scopus 로고
    • Designing Combinatorial Library Mixtures Using a Genetic Algorithm
    • Brown, R. D.; Martin, Y. C. Designing Combinatorial Library Mixtures Using a Genetic Algorithm J. Med. Chem. 1997, 40, 2304-2313
    • (1997) J. Med. Chem. , vol.40 , pp. 2304-2313
    • Brown, R.D.1    Martin, Y.C.2
  • 29
    • 0034085674 scopus 로고    scopus 로고
    • A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm
    • DOI 10.1023/A:1008108423895
    • Douguet, D.; Thoreau, E.; Grassy, G.Â. r. A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm J. Comput.-Aided Mol. Des. 2000, 14, 449-466 (Pubitemid 30386820)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.5 , pp. 449-466
    • Douguet, D.1    Thoreau, E.2    Grassy, G.3
  • 30
    • 42149174453 scopus 로고    scopus 로고
    • Fragment-based de Novo Ligand design by multiobjective evolutionary optimization
    • DOI 10.1021/ci700424b
    • Dey, F.; Caflisch, A. Fragment-based de novo ligand design by multiobjective evolutionary optimization J. Chem. Inf. Model. 2008, 48, 679-90 (Pubitemid 351535435)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.3 , pp. 679-690
    • Dey, F.1    Caflisch, A.2
  • 31
    • 0031859262 scopus 로고    scopus 로고
    • Evolutionary combinatorial chemistry: Application of genetic algorithms
    • DOI 10.1016/S1359-6446(98)01219-7, PII S1359644698012197
    • Weber, L. Evolutionary combinatorial chemistry: application of genetic algorithms Angew. Chem., Int. Ed. Engl. 1998, 107, 2 (Pubitemid 28352592)
    • (1998) Drug Discovery Today , vol.3 , Issue.8 , pp. 379-385
    • Weber, L.1
  • 36
    • 35848947985 scopus 로고    scopus 로고
    • Tagged fragment method for evolutionary structure-based de novo lead generation and optimization
    • DOI 10.1021/jm070750k
    • Liu, Q.; Masek, B.; Smith, K.; Smith, J. Tagged fragment method for evolutionary structure-based de novo lead generation and optimization J. Med. Chem. 2007, 50, 5392-402 (Pubitemid 350057850)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.22 , pp. 5392-5402
    • Liu, Q.1    Masek, B.2    Smith, K.3    Smith, J.4
  • 37
    • 0035289779 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • DOI 10.1016/S0169-409X(00)00129-0, PII S0169409X00001290
    • Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 2001, 46, 3-26 (Pubitemid 33653411)
    • (2000) Advanced Drug Delivery Reviews , vol.46 , Issue.1-3 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 39
    • 33947716119 scopus 로고    scopus 로고
    • A semiempirical free energy force field with charge-based desolvation
    • Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A semiempirical free energy force field with charge-based desolvation J. Comput. Chem. 2007, 28, 1145-52
    • (2007) J. Comput. Chem. , vol.28 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 41
    • 26444588137 scopus 로고    scopus 로고
    • CSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
    • DOI 10.1021/jm050436v
    • Velec, H. F.; Gohlke, H.; Klebe, G. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction J. Med. Chem. 2005, 48, 6296-303 (Pubitemid 41428984)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.20 , pp. 6296-6303
    • Velec, H.F.G.1    Gohlke, H.2    Klebe, G.3
  • 43
    • 0035374993 scopus 로고    scopus 로고
    • Self-adaptive genetic algorithms with simulated binary crossover
    • Deb, K.; Beyer, H. G. Self-adaptive genetic algorithms with simulated binary crossover Evol. Comput. 2001, 9, 197-221
    • (2001) Evol. Comput. , vol.9 , pp. 197-221
    • Deb, K.1    Beyer, H.G.2
  • 49
    • 77957238961 scopus 로고    scopus 로고
    • v1.5.2
    • MGLTools v1.5.2, 2009, http://mgltools.scripps.edu/.
    • (2009) MGLTools
  • 50
    • 77957242943 scopus 로고    scopus 로고
    • CCDC, 2009, http://ccdc.cam.ac.uk/products/life-sciences/gold/case- studies/gold-validation-virtual-screening.
    • (2009)
  • 51
    • 0004313709 scopus 로고    scopus 로고
    • Chemical Computing Group: Montreal, CA
    • Molecular Operating Environment; Chemical Computing Group: Montreal, CA, 2009.
    • (2009) Molecular Operating Environment
  • 52
    • 0035846071 scopus 로고    scopus 로고
    • Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitors
    • DOI 10.1021/jm010833f
    • Linusson, A.; Gottfries, J.; Olsson, T.; Ornskov, E.; Folestad, S.; Norden, B.; Wold, S. Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitors J. Med. Chem. 2001, 44, 3424-39 (Pubitemid 32947909)
    • (2001) Journal of Medicinal Chemistry , vol.44 , Issue.21 , pp. 3424-3439
    • Linusson, A.1    Gottfries, J.2    Olsson, T.3    Ornskov, E.4    Folestad, S.5    Norden, B.6    Wold, S.7
  • 53
    • 0024431034 scopus 로고
    • The refined 1.9 Å crystal structure of human α-thrombin: Interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment
    • Bode, W.; Mayr, I.; Baumann, U.; Huber, R.; Stone, S. R.; Hofsteenge, J. The refined 1.9 Å crystal structure of human α-thrombin: interaction with d -Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment EMBO J. 1989, 8, 3467-75 (Pubitemid 19273577)
    • (1989) EMBO Journal , vol.8 , Issue.11 , pp. 3467-3475
    • Bode, W.1    Mayr, I.2    Baumann, U.3    Huber, R.4    Stone, S.R.5    Hofsteenge, J.6
  • 54
    • 0028209977 scopus 로고
    • Crystallographic structures of thrombin complexed with thrombin receptor peptides: Existence of expected and novel binding modes
    • Mathews, I. I.; Padmanabhan, K. P.; Ganesh, V.; Tulinsky, A.; Ishii, M.; Chen, J.; Turck, C. W.; Coughlin, S. R.; Fenton, J. W., 2nd. Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes Biochemistry 1994, 33, 3266-79 (Pubitemid 24112639)
    • (1994) Biochemistry , vol.33 , Issue.11 , pp. 3266-3279
    • Mathews, I.I.1    Padmanabhan, K.P.2    Ganesh, V.3    Tulinsky, A.4
  • 58
    • 0028784163 scopus 로고
    • Two heads are better than one: Crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin
    • van de Locht, A.; Lamba, D.; Bauer, M.; Huber, R.; Friedrich, T.; Kroger, B.; Hoffken, W.; Bode, W. Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin EMBO J. 1995, 14, 5149-57
    • (1995) EMBO J. , vol.14 , pp. 5149-5157
    • Van De Locht, A.1    Lamba, D.2    Bauer, M.3    Huber, R.4    Friedrich, T.5    Kroger, B.6    Hoffken, W.7    Bode, W.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.