메뉴 건너뛰기




Volumn 13, Issue 4, 2010, Pages 366-374

MoStBioDat - Molecular and structural bioinformatics database

Author keywords

Chemoinformatics; HTS; Ligand; Macromolecule; PDB; Python; Relational database; SDF; SMILES

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DATA BASE; INFORMATION STORAGE; INFORMATION SYSTEM; MOLECULAR AND STRUCTURAL BIOINFORMATICS DATABASE; PRIORITY JOURNAL;

EID: 77950816830     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: 10.2174/138620710791054295     Document Type: Article
Times cited : (5)

References (55)
  • 2
    • 19644377421 scopus 로고    scopus 로고
    • Prediction methods and databases within chemoinformatics: Emphasis on drugs and drug candidates
    • Jónsdóttir, S.; Jørgensen, F.; Søren, B. Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics, 2005, 21, 2145-2160.
    • (2005) Bioinformatics , vol.21 , pp. 2145-2160
    • Jónsdóttir, S.1    Jørgensen, F.2    Søren, B.3
  • 4
    • 33244478113 scopus 로고    scopus 로고
    • Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrones as inhibitors of HIV-1 protease: An application of the Receptor-Dependent (RD) 4D-QSAR Formalism
    • DOI 10.1021/ci050326x
    • Santos-Filho, O.; Hopfinger, A. Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrones as inhibitors of HIV-1 protease: an application of the receptor dependent (RD) 4D-QSAR formalism. J. Chem. Inf. Model., 2006, 345-354. (Pubitemid 43282127)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.1 , pp. 345-354
    • Santos-Filho, O.A.1    Hopfinger, A.J.2
  • 5
    • 0043235843 scopus 로고    scopus 로고
    • Self-organizing neural networks for pharmacophore mapping
    • DOI 10.1016/S0169-409X(03)00116-9
    • Polanski, J. Self-organizing neural networks for pharmacophore mapping, Adv. Drug. Deliver. Rev., 2003, 55, 1149-1162. (Pubitemid 37098281)
    • (2003) Advanced Drug Delivery Reviews , vol.55 , Issue.9 , pp. 1149-1162
    • Polanski, J.1
  • 6
    • 27744502081 scopus 로고    scopus 로고
    • A 4D-QSAR study on anti-HIV HEPT analogues
    • DOI 10.1016/j.bmc.2005.08.023, PII S0968089605007777
    • Bak, A.; Polanski, J. The 4D-QSAR study on anti-HIV HEPT analogues. Bioorg. Med. Chem., 2006, 14, 273-279. (Pubitemid 41635489)
    • (2006) Bioorganic and Medicinal Chemistry , vol.14 , Issue.1 , pp. 273-279
    • Bak, A.1    Polanski, J.2
  • 7
    • 34547657462 scopus 로고    scopus 로고
    • Modeling robust QSAR 3: SOM-4D-QSAR with iterative variable elimination IVE-PLS: Application to steroid, azo dye, and benzoic acid series
    • DOI 10.1021/ci700025m
    • Bak, A.; Polanski, J. Modeling robust QSAR 3: SOM-4D-QSAR with iterative variable elimination IVE-PLS: application to steroid, azo dye and benzoic acid series. J. Chem. Inf. Model., 2007, 47, 1469-1480. (Pubitemid 47210050)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.4 , pp. 1469-1480
    • Bak, A.1    Polanski, J.2
  • 10
    • 27944507949 scopus 로고    scopus 로고
    • ChemDB: A public database of small molecules and related chemoinformatics resources
    • DOI 10.1093/bioinformatics/bti683
    • Chen, J.; Swamidass, S.; Dou, Y.; Bruand, J.; Baldi, P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics. 2005, 21, 4133-4139. (Pubitemid 41672103)
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4133-4139
    • Chen, J.1    Swamidass, S.J.2    Dou, Y.3    Bruand, J.4    Baldi, P.5
  • 11
    • 77950817086 scopus 로고    scopus 로고
    • http://www.ebi.ac.uk/pdbe/docs/References.html
  • 15
    • 77950821874 scopus 로고    scopus 로고
    • http://www.mysql.com/
  • 16
    • 77950844230 scopus 로고    scopus 로고
    • http://www.python.org
  • 17
    • 77950835977 scopus 로고    scopus 로고
    • http://dirac.cnrs-orleans.fr/MMTK/
  • 18
    • 77950800238 scopus 로고    scopus 로고
    • http://www.ks.uiuc.edu/Research/vmd/
  • 19
    • 77950848449 scopus 로고    scopus 로고
    • http://www.r-project.org/
  • 20
    • 26944486424 scopus 로고    scopus 로고
    • Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
    • DOI 10.1093/bioinformatics/bti1055
    • Swamidass, S.; Chen, J.; Bruand, J.; Phung, P.; Ralaivola, L.; Baldi, P. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics, 2005, 21, 359-368. (Pubitemid 41794509)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Swamidass, S.J.1    Chen, J.2    Bruand, J.3    Phung, P.4    Ralaivola, L.5    Baldi, P.6
  • 22
    • 0001708959 scopus 로고
    • Description of several chemical structure file formats used by computer programs developed at molecular design limited
    • Dalby, A.; Nourse, J.; Hounshell, W.; Gushurst, A.; Grier, D.; Leland, B.; Laufer, J. Description of several chemical structure file formats used by computer programs developed at molecular design limited. J. Chem. Inf. Comput. Sci., 1992, 32, 244-255.
    • (1992) J. Chem. Inf. Comput. Sci. , vol.32 , pp. 244-255
    • Dalby, A.1    Nourse, J.2    Hounshell, W.3    Gushurst, A.4    Grier, D.5    Leland, B.6    Laufer, J.7
  • 23
    • 0012034179 scopus 로고
    • The substance module: The representation storage and searching of complex structures
    • Hushurst, A.; Nourse, J.; Hounshell, W.; Leland, B.; Raich, D. The substance module: the representation, storage and searching of complex structures. J. Chem. Inf. Comput. Sci., 1991, 31, 447-454.
    • (1991) J. Chem. Inf. Comput. Sci. , vol.31 , pp. 447-454
    • Hushurst, A.1    Nourse, J.2    Hounshell, W.3    Leland, B.4    Raich, D.5
  • 24
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • DOI 10.1021/ci049714+
    • Irwin, J.; Shoichet, B. ZINC-A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model., 2005, 45, 177-182. (Pubitemid 40736970)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.1 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 26
    • 0034020917 scopus 로고    scopus 로고
    • STAR/mmCIF: An ontology for macromolecular structure
    • Westbrook, J.; Bourne, P. STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics, 2000, 16, 159-168. (Pubitemid 30248593)
    • (2000) Bioinformatics , vol.16 , Issue.2 , pp. 159-168
    • Westbrook, J.D.1    Bourne, P.E.2
  • 29
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • DOI 10.1093/nar/gkl971
    • Berman, H.; Henrick, K.; Nakamura, H.; Markley, J. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 2007, 35, 301-303. (Pubitemid 46056219)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 30
    • 16344364140 scopus 로고    scopus 로고
    • PDBML: The representation of archival macromolecular structure data in XML
    • DOI 10.1093/bioinformatics/bti082
    • Westbrook, J.; Ito, N.; Nakamura, H.; Henrick, K.; Berman, H. PDBML: the representation of archival macromolecular structure in XML. Bioinformatics, 2005, 21, 988-992. (Pubitemid 40467920)
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 988-992
    • Westbrook, J.1    Ito, N.2    Nakamura, H.3    Henrick, K.4    Berman, H.M.5
  • 32
    • 77950843111 scopus 로고    scopus 로고
    • http://mmcif.pdb.org/
  • 33
    • 0023965741 scopus 로고    scopus 로고
    • SMILES a chemical language and information system. 1. Introduction to methodology and encoding rules
    • Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci., 1998, 28, 31-36.
    • (1998) J. Chem. Inf. Comput. Sci. , vol.28 , pp. 31-36
    • Weininger, D.1
  • 35
    • 0000010226 scopus 로고    scopus 로고
    • Novel canonical coding method for representation of three-dimensional structures
    • Satoh, H.; Koshino, H.; Funatsu, K.; Nakata, T. Novel canonical coding method for representation of three-dimensional structures. J. Chem. Inf. Comput. Sci., 2000, 40, 622-630.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 622-630
    • Satoh, H.1    Koshino, H.2    Funatsu, K.3    Nakata, T.4
  • 36
    • 35248878598 scopus 로고    scopus 로고
    • Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmetric information
    • DOI 10.1021/ci600238j
    • Koichi, S.; Iwata, S.; Uno, T.; Koshino, H.; Satoh, H. Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmeteric information. J. Chem. Inf. Model., 2007, 45, 1734-1746. (Pubitemid 47561122)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.5 , pp. 1734-1746
    • Koichi, S.1    Iwata, S.2    Uno, T.3    Koshino, H.4    Satoh, H.5
  • 38
    • 77950793500 scopus 로고    scopus 로고
    • http://docs.python.org/tutorial/
  • 39
    • 77950852564 scopus 로고    scopus 로고
    • OEChem-Python Theory Manual, OpenEye Scientific Software Inc. 2008 Santa Fe, NM 87508
    • OEChem-Python Theory Manual, OpenEye Scientific Software Inc., 2008, Santa Fe, NM 87508.
  • 40
    • 41249091782 scopus 로고    scopus 로고
    • Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit
    • O'Boyle, N.; Morley, C.; Hutchison, R. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. Chem. Cent. J., 2008, 2, 1-7.
    • (2008) Chem. Cent. J. , vol.2 , pp. 1-7
    • O'Boyle, N.1    Morley, C.2    Hutchison, R.3
  • 41
    • 77950824496 scopus 로고    scopus 로고
    • http://soiland.no/i/src/forgetsql2/
  • 42
    • 77950832059 scopus 로고    scopus 로고
    • http://www.eyesopen.com/docs/html/api/
  • 43
    • 77950811575 scopus 로고    scopus 로고
    • http://www.sqlobject.org/SQLBuilder.html
  • 44
    • 34247228558 scopus 로고    scopus 로고
    • Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time
    • DOI 10.1021/ci600358f
    • Swamidass, S.; Baldi, P. Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sub-linear time. J. Chem. Inf. Model., 2007, 47, 302-317. (Pubitemid 46615935)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.2 , pp. 302-317
    • Swamidass, S.J.1    Baldi, P.2
  • 45
    • 20444410051 scopus 로고    scopus 로고
    • Database clustering with a combination of fingerprint and maximum common substructure methods
    • DOI 10.1021/ci050011h
    • Stahl, M.; Mauser, H. Database clustering with a combination of fingerprint and maximum common substructure methods. J. Chem. Inf. Model., 2005, 45, 542-548. (Pubitemid 40795160)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.3 , pp. 542-548
    • Stahl, M.1    Mauser, H.2
  • 46
    • 77950802067 scopus 로고    scopus 로고
    • Daylight Theory Manual, http://www.daylight.com/dayhtml/doc/theory/ theory.toc.html
    • Theory Manual, D.1
  • 47
    • 0001232509 scopus 로고    scopus 로고
    • On the properties of bit string-based measures of chemical similarity
    • Flower, D. On the properties of bit-string based measures of chemical similarity. J. Chem. Inf. Comput. Sci., 1998, 38, 379-386. (Pubitemid 128594448)
    • (1998) Journal of Chemical Information and Computer Sciences , vol.38 , Issue.3 , pp. 379-386
    • Flower, D.R.1
  • 48
    • 61949359014 scopus 로고    scopus 로고
    • Common pharmacophore identification using Frequent Clique detection algorithm
    • Podolyan, Y.; Karypis, G. Common pharmacophore identification using Frequent Clique detection algorithm. J. Chem. Inf. Model., 2009, 49, 13-21.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 13-21
    • Podolyan, Y.1    Karypis, G.2
  • 49
    • 46249123633 scopus 로고    scopus 로고
    • A maximum common substructure-based algorithm for searching and predicting drug-like compounds
    • DOI 10.1093/bioinformatics/btn186
    • Cao, Y.; Jiang, T.; Girke, T. A maximum common substructure-based algorithm for searching and predicting drug-like compounds, Bioinformatics, 2008, 24, 366-374. (Pubitemid 351911692)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Cao, Y.1    Jiang, T.2    Girke, T.3
  • 50
    • 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.; Lombardo, F.; Dominy, B.; Feeney, P. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Del. Res., 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
  • 52
    • 2942564021 scopus 로고    scopus 로고
    • Pursuing the leadlikeness concept in pharmaceutical research
    • DOI 10.1016/j.cbpa.2004.04.003, PII S1367593104000493
    • Hann, M.; Oprea, T. Pursuing the leadlikeness concept in pharmaceutical research. Curr. Opin. Chem. Biol., 2004, 8, 255-263. (Pubitemid 38759400)
    • (2004) Current Opinion in Chemical Biology , vol.8 , Issue.3 , pp. 255-263
    • Hann, M.M.1    Oprea, T.I.2
  • 53
    • 77950789490 scopus 로고    scopus 로고
    • http://openbabel.org/wiki/Main-Page
  • 54
    • 77950843838 scopus 로고    scopus 로고
    • http://www.eyesopen.com/
  • 55
    • 70349554501 scopus 로고    scopus 로고
    • The use of MoStBioDat for rapid screening of molecular diversity
    • Bak, A.; Polanski, J.; Kurczyk, A. The use of MoStBioDat for rapid screening of molecular diversity. Molecules, 2009, 14, 3436-3445.
    • (2009) Molecules , vol.14 , pp. 3436-3445
    • Bak, A.1    Polanski, J.2    Kurczyk, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.