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Volumn 11, Issue 3, 2008, Pages 311-319

Bioinformatics and cheminformatics: Where do the twain meet?

Author keywords

Bioinformatics; Biological networks; Cheminformatics; Data fusion; QSAR; similarity assessment

Indexed keywords

BIOINFORMATICS; CHEMINFORMATICS; DNA SEQUENCE; INFORMATION PROCESSING; NONHUMAN; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; REVIEW; SYSTEMS BIOLOGY;

EID: 42449139640     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review
Times cited : (15)

References (108)
  • 1
    • 33846863801 scopus 로고    scopus 로고
    • Radial clustergrams: Visualizing the aggregate properties of heirarchical clusters
    • Agrafiotis DK, Bandyopadhyay D, Farnum M: Radial clustergrams: Visualizing the aggregate properties of heirarchical clusters. J Chem Inf Model (2007) 47(1):69-75.
    • (2007) J Chem Inf Model , vol.47 , Issue.1 , pp. 69-75
    • Agrafiotis, D.K.1    Bandyopadhyay, D.2    Farnum, M.3
  • 4
    • 33947245022 scopus 로고    scopus 로고
    • Evaluation of machine-learning methods for ligand-based virtual screening
    • Describes the exploration of similarity, kernel and fusion methods in virtual high-throughput screens, •
    • Chen B, Harrison RF, Papadatos G, Willett P, Wood DJ, Lewell XQ, Greenidge P, Stiefl N: Evaluation of machine-learning methods for ligand-based virtual screening. J Comput Aided Mol Des (2007) 21(1-3):53-62. • Describes the exploration of similarity, kernel and fusion methods in virtual high-throughput screens.
    • (2007) J Comput Aided Mol Des , vol.21 , Issue.1-3 , pp. 53-62
    • Chen, B.1    Harrison, R.F.2    Papadatos, G.3    Willett, P.4    Wood, D.J.5    Lewell, X.Q.6    Greenidge, P.7    Stiefl, N.8
  • 5
    • 34848837283 scopus 로고    scopus 로고
    • Classification of heterogeneous microarray data by maximum entropy kernel
    • Demonstrates that kernel entropy maximization improved robustness and prediction accuracy on heterogenous microarray data, •
    • Fujibuchi W, Kato T: Classification of heterogeneous microarray data by maximum entropy kernel. BMC Bioinform (2007) 8:267. • Demonstrates that kernel entropy maximization improved robustness and prediction accuracy on heterogenous microarray data.
    • (2007) BMC Bioinform , vol.8 , pp. 267
    • Fujibuchi, W.1    Kato, T.2
  • 6
    • 37249009571 scopus 로고    scopus 로고
    • Kernel approach to molecular similarity based on iterative graph similarity
    • Rupp M, Proschak E, Schneider G: Kernel approach to molecular similarity based on iterative graph similarity. J Chem Inf Model (2007) 47(6):2280-2286.
    • (2007) J Chem Inf Model , vol.47 , Issue.6 , pp. 2280-2286
    • Rupp, M.1    Proschak, E.2    Schneider, G.3
  • 7
    • 33646568805 scopus 로고    scopus 로고
    • Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P et al: Gene prioritization through genomic data fusion. Nat Biotechnol (2006) 24(5):537-544. • Describes how the authors greatly improved their ability to prioritize genes implicated in disease by using data fusion and order statistics.
    • Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P et al: Gene prioritization through genomic data fusion. Nat Biotechnol (2006) 24(5):537-544. • Describes how the authors greatly improved their ability to prioritize genes implicated in disease by using data fusion and order statistics.
  • 8
    • 33646249968 scopus 로고    scopus 로고
    • Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A: New methods for ligand-based virtual screening: Use of data fusion and machine learning to enhance the effectiveness of similarity searching. J Chem Inf Model (2006) 46(2):462-470. •• Describes how group fusion (the use of several bioactive reference structures and the assumption that nearest neighbors in similarity space are also active) was shown to improve upon existing molecular similarity searching methods.
    • Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A: New methods for ligand-based virtual screening: Use of data fusion and machine learning to enhance the effectiveness of similarity searching. J Chem Inf Model (2006) 46(2):462-470. •• Describes how group fusion (the use of several bioactive reference structures and the assumption that nearest neighbors in similarity space are also active) was shown to improve upon existing molecular similarity searching methods.
  • 9
    • 38149020108 scopus 로고    scopus 로고
    • Data fusion and auto-fusion for quantitative structure-activity relationships (QSAR). In: Artificial Neural Networks - ICANN 2007. 17th International Conference, Porto, Portugal, September 9-13, 2007
    • Eds, Springer Berlin, Heidelberg, Germany
    • Huang C, Embrechts MJ, Sukumar N, Breneman CM: Data fusion and auto-fusion for quantitative structure-activity relationships (QSAR). In: Artificial Neural Networks - ICANN 2007. 17th International Conference, Porto, Portugal, September 9-13, 2007, Proceedings, Part I. Marques de Sá J, Alexandre LA, Duch W, Mandic D (Eds), Springer Berlin, Heidelberg, Germany (2007):628-637.
    • (2007) Proceedings, Part I. Marques de Sá J, Alexandre LA, Duch W, Mandic , vol.500 , pp. 628-637
    • Huang, C.1    Embrechts, M.J.2    Sukumar, N.3    Breneman, C.M.4
  • 10
    • 0033669056 scopus 로고    scopus 로고
    • Combination of molecular similarity measures using data fusion
    • Ginn CMR, Willett P, Bradshaw J: Combination of molecular similarity measures using data fusion. Perspec Drug Disc Des (2000) 20(1):1-16.
    • (2000) Perspec Drug Disc Des , vol.20 , Issue.1 , pp. 1-16
    • Ginn, C.M.R.1    Willett, P.2    Bradshaw, J.3
  • 12
    • 0036355686 scopus 로고    scopus 로고
    • Integration of genomic datasets to predict protein complexes in yeast
    • Jansen R, Lan N, Qian J, Gerstein M: Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics (2002) 2(2):71-81.
    • (2002) J Struct Funct Genomics , vol.2 , Issue.2 , pp. 71-81
    • Jansen, R.1    Lan, N.2    Qian, J.3    Gerstein, M.4
  • 13
    • 33244486343 scopus 로고    scopus 로고
    • Combining chemodescriptors and biodescriptors in quantitative structure-activity relationship modeling
    • Demonstrates that the fusion of traditional chemical descriptors with biological descriptors has improved toxicity predictions, •
    • Hawkins DM, Basak SC, Kraker J, Geiss KT, Witzmann FA: Combining chemodescriptors and biodescriptors in quantitative structure-activity relationship modeling. J Chem Inf Model (2006) 46(1):9-16. • Demonstrates that the fusion of traditional chemical descriptors with biological descriptors has improved toxicity predictions.
    • (2006) J Chem Inf Model , vol.46 , Issue.1 , pp. 9-16
    • Hawkins, D.M.1    Basak, S.C.2    Kraker, J.3    Geiss, K.T.4    Witzmann, F.A.5
  • 14
    • 0141561891 scopus 로고    scopus 로고
    • Ge H, Walhout AJ, Vidal M: Integrating 'omic' information: A bridge between genomics and systems biology. Trends Genet (2003) 19(10):551-560. • Demonstrates that the fusion of 'omic' data from multiple sources has increased the reliability of correlations found in gene function annotation.
    • Ge H, Walhout AJ, Vidal M: Integrating 'omic' information: A bridge between genomics and systems biology. Trends Genet (2003) 19(10):551-560. • Demonstrates that the fusion of 'omic' data from multiple sources has increased the reliability of correlations found in gene function annotation.
  • 15
    • 33646561524 scopus 로고    scopus 로고
    • Complex graph matrix representations and characterizations of proteomic maps and chemically induced changes to proteomes
    • Describes how graph theory was used to construct proteomic maps and define an adjacency matrix from 2D (mass and charge) gels, •
    • Balasubramanian K, Khokhani K, Basak SC: Complex graph matrix representations and characterizations of proteomic maps and chemically induced changes to proteomes. J Proteome Res (2006) 5(5):1133-1142. • Describes how graph theory was used to construct proteomic maps and define an adjacency matrix from 2D (mass and charge) gels.
    • (2006) J Proteome Res , vol.5 , Issue.5 , pp. 1133-1142
    • Balasubramanian, K.1    Khokhani, K.2    Basak, S.C.3
  • 16
    • 0037434977 scopus 로고    scopus 로고
    • Biomedical informatics for proteomics
    • Argues that the field of proteomics needs to address biological variability, pre-analytic factors and the lack of analytical reproducibility as a necessity for obtaining predictive models, •
    • Boguski MS, McIntosh MW: Biomedical informatics for proteomics. Nature (2003) 422(6928):233-237. • Argues that the field of proteomics needs to address biological variability, pre-analytic factors and the lack of analytical reproducibility as a necessity for obtaining predictive models.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 233-237
    • Boguski, M.S.1    McIntosh, M.W.2
  • 17
    • 0037305947 scopus 로고    scopus 로고
    • Ontologies for proteomics: Towards a systematic definition of structure and function that scales to the genome level
    • Lan N, Montelione GT, Gerstein M: Ontologies for proteomics: Towards a systematic definition of structure and function that scales to the genome level. Curr Opin Chem Biol (2003) 7(1): 44-54.
    • (2003) Curr Opin Chem Biol , vol.7 , Issue.1 , pp. 44-54
    • Lan, N.1    Montelione, G.T.2    Gerstein, M.3
  • 18
    • 0035438393 scopus 로고    scopus 로고
    • On graphical and numerical characterization of proteomics maps
    • Randić M: On graphical and numerical characterization of proteomics maps. J Chem Inf Comput Sci (2001) 41(5):1330-1338.
    • (2001) J Chem Inf Comput Sci , vol.41 , Issue.5 , pp. 1330-1338
    • Randić, M.1
  • 19
    • 0037108167 scopus 로고    scopus 로고
    • A graph theoretical characterization of proteomics maps
    • Randić M: A graph theoretical characterization of proteomics maps. Int J Quantum Chem (2002) 90(2):848-858.
    • (2002) Int J Quantum Chem , vol.90 , Issue.2 , pp. 848-858
    • Randić, M.1
  • 20
    • 2942541277 scopus 로고    scopus 로고
    • Predicting co-complexed protein pairs using genomic and proteomic data integration
    • Zhang LV, Wong SL, King OD, Roth FP: Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinform (2004) 5:38.
    • (2004) BMC Bioinform , vol.5 , pp. 38
    • Zhang, L.V.1    Wong, S.L.2    King, O.D.3    Roth, F.P.4
  • 21
    • 27444447278 scopus 로고    scopus 로고
    • Biospectra analysis: Model proteome characterization for linking molecular structure and biological response
    • Describes the classification of molecules through hierarchal clustering and bioassay inhibition profiling, •
    • Fliri AF, Loging WT, Thadeio PF, Volkmann RA: Biospectra analysis: Model proteome characterization for linking molecular structure and biological response. J Med Chem (2005) 48(22):6918-6925. • Describes the classification of molecules through hierarchal clustering and bioassay inhibition profiling.
    • (2005) J Med Chem , vol.48 , Issue.22 , pp. 6918-6925
    • Fliri, A.F.1    Loging, W.T.2    Thadeio, P.F.3    Volkmann, R.A.4
  • 22
    • 35148838537 scopus 로고    scopus 로고
    • Yildirim MA, Goh K-I, Cusick ME, Barabási A-L, Vidal M: Drug-target network. Nat Biotechnol (2007) 25(10):1119- 1126. • Demonstrates how FDA-approved drugs and their targets were used to construct a bipartite graph of protein-drug interactions, which was then decomposed into two network projections: a drug network and a complementary target protein network. Strong local clustering of drugs and a recent slow trend toward greater promiscuity and more diversified targets was noted.
    • Yildirim MA, Goh K-I, Cusick ME, Barabási A-L, Vidal M: Drug-target network. Nat Biotechnol (2007) 25(10):1119- 1126. • Demonstrates how FDA-approved drugs and their targets were used to construct a bipartite graph of protein-drug interactions, which was then decomposed into two network projections: a drug network and a complementary target protein network. Strong local clustering of drugs and a recent slow trend toward greater promiscuity and more diversified targets was noted.
  • 23
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • Describes the construction of a cartographic representation of metabolic networks for 12 organisms, which showed a modular structure with metabolites connecting different modules being more strongly conserved than within-module hubs, •
    • Guimerà R, Nunes Amaral LA: Functional cartography of complex metabolic networks. Nature (2005) 433(7028):895-900. • Describes the construction of a cartographic representation of metabolic networks for 12 organisms, which showed a modular structure with metabolites connecting different modules being more strongly conserved than within-module hubs.
    • (2005) Nature , vol.433 , Issue.7028 , pp. 895-900
    • Guimerà, R.1    Nunes Amaral, L.A.2
  • 24
    • 36349034517 scopus 로고    scopus 로고
    • Laederach A: Informatics challenges in structured RNA. Briefings Bioinform (2007) 8(5):294-303. • Points of interest include folding dynamics and nucleic acid recognition in RNA interference.
    • Laederach A: Informatics challenges in structured RNA. Briefings Bioinform (2007) 8(5):294-303. • Points of interest include folding dynamics and nucleic acid recognition in RNA interference.
  • 25
    • 33745135773 scopus 로고    scopus 로고
    • Recent developments of the Chemistry Development Kit (CDK) - An open-source Java library for chemo- and bioinformatics
    • Describes new biologically and chemically relevant features of the opensource software toolkit CDK, •
    • Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL: Recent developments of the Chemistry Development Kit (CDK) - An open-source Java library for chemo- and bioinformatics. Curr Pharm Design (2006) 12(17):2111-2120. • Describes new biologically and chemically relevant features of the opensource software toolkit CDK.
    • (2006) Curr Pharm Design , vol.12 , Issue.17 , pp. 2111-2120
    • Steinbeck, C.1    Hoppe, C.2    Kuhn, S.3    Floris, M.4    Guha, R.5    Willighagen, E.L.6
  • 26
    • 36349009372 scopus 로고    scopus 로고
    • Ballester PJ, Richards WG: Ultrafast shape recognition for similarity search in molecular databases. Proc R Soc A (2007) 463(2081):1307-1321.
    • Ballester PJ, Richards WG: Ultrafast shape recognition for similarity search in molecular databases. Proc R Soc A (2007) 463(2081):1307-1321.
  • 27
    • 34547260921 scopus 로고    scopus 로고
    • Ultrafast shape recognition to search compound databases for similar molecular shapes
    • USR is a rapid, alignment-free similarity measure based on molecular shape moments, which demonstrated good performance at shape classification, •
    • Ballester PJ, Richards WG: Ultrafast shape recognition to search compound databases for similar molecular shapes. J Comput Chem (2007) 28(10):1711-1723. • USR is a rapid, alignment-free similarity measure based on molecular shape moments, which demonstrated good performance at shape classification.
    • (2007) J Comput Chem , vol.28 , Issue.10 , pp. 1711-1723
    • Ballester, P.J.1    Richards, W.G.2
  • 28
    • 33750336399 scopus 로고    scopus 로고
    • Lingos, finite state machines and fast similarity searching
    • Introduces the Lingo method, based on encoding molecular structure into canonical SMILES strings, which were decomposed into a set of overlapping character sub-strings. Molecular similarity assessment is therefore reduced to comparing Lingos, •
    • Grant JA, Haigh JA, Pickup BT, Nicholls A, Sayle RA: Lingos, finite state machines and fast similarity searching. J Chem Inf Model (2006) 46(5):1912-1918. • Introduces the Lingo method, based on encoding molecular structure into canonical SMILES strings, which were decomposed into a set of overlapping character sub-strings. Molecular similarity assessment is therefore reduced to comparing Lingos.
    • (2006) J Chem Inf Model , vol.46 , Issue.5 , pp. 1912-1918
    • Grant, J.A.1    Haigh, J.A.2    Pickup, B.T.3    Nicholls, A.4    Sayle, R.A.5
  • 29
    • 0141828504 scopus 로고    scopus 로고
    • Protein structure-similarity as guiding principle for combinatorial library design
    • Koch MA, Breinbauer R, Waldmann H: Protein structure-similarity as guiding principle for combinatorial library design. Biol Chem (2003) 384(9):1265-1272.
    • (2003) Biol Chem , vol.384 , Issue.9 , pp. 1265-1272
    • Koch, M.A.1    Breinbauer, R.2    Waldmann, H.3
  • 30
    • 33846881809 scopus 로고    scopus 로고
    • Similarity by compression
    • Demonstrates the use of a novel similarity score: the normalized compression distance as a complementary alternative to Tanimoto similarity, ••
    • Melville JL, Riley JF, Hirst JD: Similarity by compression. J Chem Inf Model (2007) 47(1):25-33. •• Demonstrates the use of a novel similarity score: the normalized compression distance as a complementary alternative to Tanimoto similarity.
    • (2007) J Chem Inf Model , vol.47 , Issue.1 , pp. 25-33
    • Melville, J.L.1    Riley, J.F.2    Hirst, J.D.3
  • 31
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: A key technique in molecular informatics
    • Bender A, Glen RC: Molecular similarity: A key technique in molecular informatics. Org Biomol Chem (2004) 2(22):3204-3218.
    • (2004) Org Biomol Chem , vol.2 , Issue.22 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 32
    • 26944443036 scopus 로고    scopus 로고
    • Bender A, Glen RC: A discussion of measures of enrichment in virtual screening: Comparing the information content of descriptors with increasing levels of sophistication. J Chem Inf Model (2005) 45(5):1369-1375. • Discusses the efficacy and performance of different molecular descriptors in virtual high-throughput screens. Compared with simple molecular descriptors (such as atom and bond counts), 2D fingerprints were found to enrich only by a factor of two, with often no improvement seen in VHTS screening modes.
    • Bender A, Glen RC: A discussion of measures of enrichment in virtual screening: Comparing the information content of descriptors with increasing levels of sophistication. J Chem Inf Model (2005) 45(5):1369-1375. • Discusses the efficacy and performance of different molecular descriptors in virtual high-throughput screens. Compared with simple molecular descriptors (such as atom and bond counts), 2D fingerprints were found to enrich only by a factor of two, with often no improvement seen in VHTS screening modes.
  • 33
    • 77956726346 scopus 로고    scopus 로고
    • Molecular similarity: Advances in methods, applications, and validations in virtual screening and QSAR
    • Provides a good introductory review of molecular similarity and QSARs, •
    • Bender A, Jenkins JL, Li Q, Adams SE, Cannon EO, Glen RC: Molecular similarity: Advances in methods, applications, and validations in virtual screening and QSAR. Ann Rep Comp Chem (2006) 188(2):141-168. • Provides a good introductory review of molecular similarity and QSARs.
    • (2006) Ann Rep Comp Chem , vol.188 , Issue.2 , pp. 141-168
    • Bender, A.1    Jenkins, J.L.2    Li, Q.3    Adams, S.E.4    Cannon, E.O.5    Glen, R.C.6
  • 34
    • 1842690601 scopus 로고    scopus 로고
    • Molecular similarity searching using atom environments, information-based feature selection, and a naïve Bayesian classifier
    • Bender A, Mussa HY, Glen RC, Reiling S: Molecular similarity searching using atom environments, information-based feature selection, and a naïve Bayesian classifier. J Chem Inf Comput Sci (2004) 44(1):170-178.
    • (2004) J Chem Inf Comput Sci , vol.44 , Issue.1 , pp. 170-178
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3    Reiling, S.4
  • 35
    • 0029030747 scopus 로고
    • Molecular similarity matrices and quantitative structure-activity relationships: A case study with methodological implications
    • Benigni R, Cotta-Ramusino M, Giorgi F, Gallo G: Molecular similarity matrices and quantitative structure-activity relationships: A case study with methodological implications. J Med Chem (1995) 38(4):629-635.
    • (1995) J Med Chem , vol.38 , Issue.4 , pp. 629-635
    • Benigni, R.1    Cotta-Ramusino, M.2    Giorgi, F.3    Gallo, G.4
  • 36
    • 10244222365 scopus 로고    scopus 로고
    • Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
    • Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A: Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org Biomol Chem (2004) 2(22):3256-3266.
    • (2004) Org Biomol Chem , vol.2 , Issue.22 , pp. 3256-3266
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 37
    • 2942700377 scopus 로고    scopus 로고
    • Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures
    • Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A: Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J Chem Inf Comput Sci (2004) 44(3):1177-1185.
    • (2004) J Chem Inf Comput Sci , vol.44 , Issue.3 , pp. 1177-1185
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 38
    • 33646493006 scopus 로고    scopus 로고
    • Scaffold-hopping potential of ligand-based similarity concepts
    • Renner S, Schneider G: Scaffold-hopping potential of ligand-based similarity concepts. ChemMedChem (2006) 1(2):181-185.
    • (2006) ChemMedChem , vol.1 , Issue.2 , pp. 181-185
    • Renner, S.1    Schneider, G.2
  • 39
    • 1842532337 scopus 로고    scopus 로고
    • Chemogenomics: An emerging strategy for rapid target and drug discovery
    • Bredel M, Jacoby E: Chemogenomics: An emerging strategy for rapid target and drug discovery. Nat Rev Genet (2004) 5(4):262-275.
    • (2004) Nat Rev Genet , vol.5 , Issue.4 , pp. 262-275
    • Bredel, M.1    Jacoby, E.2
  • 40
    • 4043121114 scopus 로고    scopus 로고
    • Computational chemogenomics approaches to systematic knowledge-based drug discovery
    • Mestres J: Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discovery Dev (2004) 7(3):304-313.
    • (2004) Curr Opin Drug Discovery Dev , vol.7 , Issue.3 , pp. 304-313
    • Mestres, J.1
  • 42
    • 34547655858 scopus 로고    scopus 로고
    • Recent advances in cheminformatics
    • Presents new developments in molecular mining, structure-activity relationships, chemogenomics and de novo and fragment-based molecular design, •
    • Agrafiotis DK, Bandyopadhyay D, Wegner JK, van Vlijmen H: Recent advances in cheminformatics. J Chem Inf Model (2007) 47(4):1279-1293. • Presents new developments in molecular mining, structure-activity relationships, chemogenomics and de novo and fragment-based molecular design.
    • (2007) J Chem Inf Model , vol.47 , Issue.4 , pp. 1279-1293
    • Agrafiotis, D.K.1    Bandyopadhyay, D.2    Wegner, J.K.3    van Vlijmen, H.4
  • 43
    • 33748792021 scopus 로고    scopus 로고
    • Bio-ontologies: Current trends and future directions
    • Indicates that the future of bio-ontologies will be in certification, validation and continued cross-linking of ontological definitions through collaboration, •
    • Bodenreider O, Stevens R: Bio-ontologies: Current trends and future directions. Briefings Bioinform (2007) 7(3):256-274. • Indicates that the future of bio-ontologies will be in certification, validation and continued cross-linking of ontological definitions through collaboration.
    • (2007) Briefings Bioinform , vol.7 , Issue.3 , pp. 256-274
    • Bodenreider, O.1    Stevens, R.2
  • 44
    • 0034332545 scopus 로고    scopus 로고
    • Stevens R, Goble CA, Bechhofer S: Ontology-based knowledge representation for bioinformatics. Briefings Bioinform (2000) 1(4):398-414. • Describes ontologies in bioinformatics.
    • Stevens R, Goble CA, Bechhofer S: Ontology-based knowledge representation for bioinformatics. Briefings Bioinform (2000) 1(4):398-414. • Describes ontologies in bioinformatics.
  • 45
    • 33748847737 scopus 로고    scopus 로고
    • The life sciences semantic web is full of creeps!
    • Focuses on the feature creep of online biological repositories and their future in the semantic web, •
    • Good BM, Wilkinson MD: The life sciences semantic web is full of creeps! Briefings Bioinform (2006) 7(3):275-286. • Focuses on the feature creep of online biological repositories and their future in the semantic web.
    • (2006) Briefings Bioinform , vol.7 , Issue.3 , pp. 275-286
    • Good, B.M.1    Wilkinson, M.D.2
  • 46
    • 23844461922 scopus 로고    scopus 로고
    • Zimmermann M, Fluck J, Thi LT, Kolárik C, Kumpf K, Hofmann M: Information extraction in the life sciences: Perspectives for medicinal chemistry, pharmacology and toxicology. Curr Top Med Chem (2005) 5(8):785-796. • Focuses on the future of cheminformatics in medicinal chemistry, including structure-activity relationships, semantic linking of biological activity with chemical structure and multimodal information extraction.
    • Zimmermann M, Fluck J, Thi LT, Kolárik C, Kumpf K, Hofmann M: Information extraction in the life sciences: Perspectives for medicinal chemistry, pharmacology and toxicology. Curr Top Med Chem (2005) 5(8):785-796. • Focuses on the future of cheminformatics in medicinal chemistry, including structure-activity relationships, semantic linking of biological activity with chemical structure and multimodal information extraction.
  • 48
    • 0034040680 scopus 로고    scopus 로고
    • An ontology for biological function based on molecular interactions
    • Karp PD: An ontology for biological function based on molecular interactions. Bioinformatics (2000) 16(3):269-285.
    • (2000) Bioinformatics , vol.16 , Issue.3 , pp. 269-285
    • Karp, P.D.1
  • 50
    • 5344268130 scopus 로고    scopus 로고
    • Annotating and mining the ligandtarget chemogenomics knowledge space
    • Schuffenhauer A, Jacoby E: Annotating and mining the ligandtarget chemogenomics knowledge space. Drug Disc Today (2004) 2(5):190-200.
    • (2004) Drug Disc Today , vol.2 , Issue.5 , pp. 190-200
    • Schuffenhauer, A.1    Jacoby, E.2
  • 51
    • 34250835708 scopus 로고    scopus 로고
    • From molecular to biological structure and back
    • Provides an excellent survey of graph theoretical methods in biology and cheminformatics, with a comparative analysis of the topological structures of molecular graphs and biological networks, ••
    • Bonchev D, Buck GA: From molecular to biological structure and back. J Chem Inf Model (2007) 47(3):909-917. •• Provides an excellent survey of graph theoretical methods in biology and cheminformatics, with a comparative analysis of the topological structures of molecular graphs and biological networks.
    • (2007) J Chem Inf Model , vol.47 , Issue.3 , pp. 909-917
    • Bonchev, D.1    Buck, G.A.2
  • 52
    • 0035042776 scopus 로고    scopus 로고
    • Jenssen T-K, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet (2001) 28(1):21-28. • Seminal article that introduced PubGene, a crosslinked database that used text mining to link gene and protein names to help visualize and thus elucidate connections between genes and proteins, and the underlying meaning of such relationships.
    • Jenssen T-K, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet (2001) 28(1):21-28. • Seminal article that introduced PubGene, a crosslinked database that used text mining to link gene and protein names to help visualize and thus elucidate connections between genes and proteins, and the underlying meaning of such relationships.
  • 53
    • 42149182005 scopus 로고    scopus 로고
    • The Gene Ontology: Gene Ontology Consortium (2007). www.geneontology.org
    • (2007) The Gene Ontology
  • 54
    • 42449153872 scopus 로고    scopus 로고
    • Bethesda, MD, USA
    • PubMed: National Center for Biotechnology Information, Bethesda, MD, USA (2007). www.ncbi.nlm.nih.gov/PubMed
    • (2007)
  • 55
    • 34249752597 scopus 로고    scopus 로고
    • Quackenbush J: Extracting biology from high-dimensional biological data. J Exp Biol (2007) 210(Pt 9):1507-1517. • Describes the incorporation of heterogenous biological information to constrain model topologies, bringing the idea of predictive biology closer.
    • Quackenbush J: Extracting biology from high-dimensional biological data. J Exp Biol (2007) 210(Pt 9):1507-1517. • Describes the incorporation of heterogenous biological information to constrain model topologies, bringing the idea of predictive biology closer.
  • 56
    • 38549151817 scopus 로고    scopus 로고
    • Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M: DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res (2008) 36(Database issue):D901-D906.
    • Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M: DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res (2008) 36(Database issue):D901-D906.
  • 57
    • 0040920369 scopus 로고    scopus 로고
    • McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD and National Center for Biotechnology Information, Bethesda, MD, USA
    • Online Mendelian Inheritance in Man, OMIM™. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD and National Center for Biotechnology Information, Bethesda, MD, USA (2008). www.ncbi.nlm.nih.gov/omim
    • (2008) Online Mendelian Inheritance in Man, OMIM™
  • 58
    • 33244482490 scopus 로고    scopus 로고
    • Correlation of side-chain hubs with the functional residues in DNA-binding protein structures
    • Sathyapriya R, Brinda KV, Vishveshwara S: Correlation of side-chain hubs with the functional residues in DNA-binding protein structures. J Chem Inf Model (2006) 46(1):123-129.
    • (2006) J Chem Inf Model , vol.46 , Issue.1 , pp. 123-129
    • Sathyapriya, R.1    Brinda, K.V.2    Vishveshwara, S.3
  • 59
    • 33845875196 scopus 로고    scopus 로고
    • Relating three-dimensional structures to protein networks provides evolutionary insights
    • Provides an analysis of hubs in protein-interaction networks, demonstrating the small-world property exhibited by these networks. Multi-interface hubs were shown to evolve more slowly and hypothesized to be more highly integrated into cellular networks than single-interface hubs, •
    • Kim PM, Lu LJ, Xia Y, Gerstein MB: Relating three-dimensional structures to protein networks provides evolutionary insights. Science (2006) 314(5807):1938-1941. • Provides an analysis of hubs in protein-interaction networks, demonstrating the small-world property exhibited by these networks. Multi-interface hubs were shown to evolve more slowly and hypothesized to be more highly integrated into cellular networks than single-interface hubs.
    • (2006) Science , vol.314 , Issue.5807 , pp. 1938-1941
    • Kim, P.M.1    Lu, L.J.2    Xia, Y.3    Gerstein, M.B.4
  • 60
    • 33749508463 scopus 로고    scopus 로고
    • Characterization and prediction of protein-protein interactions within and between complexes
    • Describes the analysis of protein interactions in yeast by measuring the sequence, genomic, transcriptomic and proteomic attributes of each interacting pair, and the derivation of a predicted algorithm for identifying intra-complex interactions from other binary interactions, •
    • Sprinzak E, Altuvia Y, Margalit H: Characterization and prediction of protein-protein interactions within and between complexes. Proc Natl Acad Sci USA (2006) 103(40):14718-14723. • Describes the analysis of protein interactions in yeast by measuring the sequence, genomic, transcriptomic and proteomic attributes of each interacting pair, and the derivation of a predicted algorithm for identifying intra-complex interactions from other binary interactions.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.40 , pp. 14718-14723
    • Sprinzak, E.1    Altuvia, Y.2    Margalit, H.3
  • 61
    • 0034784262 scopus 로고    scopus 로고
    • The connectivity index 25 years after
    • Randić M: The connectivity index 25 years after. J Mol Graph Model (2001) 20(1):19-35.
    • (2001) J Mol Graph Model , vol.20 , Issue.1 , pp. 19-35
    • Randić, M.1
  • 62
    • 1842689997 scopus 로고    scopus 로고
    • Wiener-Hosoya index: A novel graph theoretical molecular descriptor
    • Randić M: Wiener-Hosoya index: A novel graph theoretical molecular descriptor. J Chem Inf Comput Sci (2004) 44(2):373-377.
    • (2004) J Chem Inf Comput Sci , vol.44 , Issue.2 , pp. 373-377
    • Randić, M.1
  • 63
    • 34548741373 scopus 로고    scopus 로고
    • Human genome encodes many proteins with charge periodicity of 28 residues
    • Ke R, Sakiyama N, Sawada R, Sonoyama M, Mitaku S: Human genome encodes many proteins with charge periodicity of 28 residues. Jap J App Phys (2007) 46(9A):6083-6086.
    • (2007) Jap J App Phys , vol.46 , Issue.9 A , pp. 6083-6086
    • Ke, R.1    Sakiyama, N.2    Sawada, R.3    Sonoyama, M.4    Mitaku, S.5
  • 64
    • 22144474037 scopus 로고    scopus 로고
    • Towards the chemometric dissection of peptide-HLA-A*0201 binding affinity: Comparison of local and global QSAR models
    • Doytchinova IA, Walshe V, Borrow P, Flower DR: Towards the chemometric dissection of peptide-HLA-A*0201 binding affinity: Comparison of local and global QSAR models. J Comput Aided Mol Des (2005) 19(3):203-212.
    • (2005) J Comput Aided Mol Des , vol.19 , Issue.3 , pp. 203-212
    • Doytchinova, I.A.1    Walshe, V.2    Borrow, P.3    Flower, D.R.4
  • 66
    • 33746156959 scopus 로고    scopus 로고
    • Paolini GV, Shapland RH, van Hoorn WP, Mason JS, Hopkins AL: Global mapping of pharmacological space. Nat Biotechnol (2006) 24(7):805-815. • Describes database integration that provides a glimpse of where the future of readily available public sector technologies may lie. The relationships between molecular properties and target class, industrial trends and attrition, and degrees of druggability are monitored.
    • Paolini GV, Shapland RH, van Hoorn WP, Mason JS, Hopkins AL: Global mapping of pharmacological space. Nat Biotechnol (2006) 24(7):805-815. • Describes database integration that provides a glimpse of where the future of readily available public sector technologies may lie. The relationships between molecular properties and target class, industrial trends and attrition, and degrees of druggability are monitored.
  • 67
    • 33646251585 scopus 로고    scopus 로고
    • Chemometric analysis of ligand receptor complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)
    • Oloff S, Zhang S, Sukumar N, Breneman C, Tropsha A: Chemometric analysis of ligand receptor complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI). J Chem Inf Model (2006) 46(2):844-851.
    • (2006) J Chem Inf Model , vol.46 , Issue.2 , pp. 844-851
    • Oloff, S.1    Zhang, S.2    Sukumar, N.3    Breneman, C.4    Tropsha, A.5
  • 68
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based 3D scaffold-hopping method and its application to a bacterial protein-protein interaction
    • Rush TS III, Grant JA, Mosyak L, Nicholls A: A shape-based 3D scaffold-hopping method and its application to a bacterial protein-protein interaction. J Med Chem (2005) 48(5):1489-1495.
    • (2005) J Med Chem , vol.48 , Issue.5 , pp. 1489-1495
    • Rush III, T.S.1    Grant, J.A.2    Mosyak, L.3    Nicholls, A.4
  • 69
    • 13844306520 scopus 로고    scopus 로고
    • Enrichment of ligands for the serotonin receptor using the shape signatures approach
    • Nagarajan K, Zauhar R, Welsh WJ: Enrichment of ligands for the serotonin receptor using the shape signatures approach. J Chem Inf Model (2005) 45(1):49-57.
    • (2005) J Chem Inf Model , vol.45 , Issue.1 , pp. 49-57
    • Nagarajan, K.1    Zauhar, R.2    Welsh, W.J.3
  • 70
    • 0345735309 scopus 로고    scopus 로고
    • Shape signatures: A new approach to computer-aided ligand- and receptor-based drug design
    • Zauhar R, Moyna G, Tian L, Li Z, Welsh WJ: Shape signatures: A new approach to computer-aided ligand- and receptor-based drug design. J Med Chem (2003) 46(26):5674-5690.
    • (2003) J Med Chem , vol.46 , Issue.26 , pp. 5674-5690
    • Zauhar, R.1    Moyna, G.2    Tian, L.3    Li, Z.4    Welsh, W.J.5
  • 72
    • 38549107118 scopus 로고    scopus 로고
    • Context shapes: Efficient complementary shape matching for protein-protein docking
    • Addresses the molecular surface encoding problem by introducing Boolean shape descriptors that are context shapes encoding the local shape for partial complementary shape matching. Hierarchical features make the method amenable for use in rapid docking and screening, •
    • Shentu Z, Al Hasan M, Bystroff C, Zaki MJ: Context shapes: Efficient complementary shape matching for protein-protein docking. Proteins (2008) 70(3):1056-1073. • Addresses the molecular surface encoding problem by introducing Boolean shape descriptors that are context shapes encoding the local shape for partial complementary shape matching. Hierarchical features make the method amenable for use in rapid docking and screening.
    • (2008) Proteins , vol.70 , Issue.3 , pp. 1056-1073
    • Shentu, Z.1    Al Hasan, M.2    Bystroff, C.3    Zaki, M.J.4
  • 73
    • 42449123157 scopus 로고    scopus 로고
    • Analysis of odor structure relationships using electronic Van der Waals surface property descriptors and genetic algorithms
    • Lavine BK Ed, American Chemical Society, Washington, DC, USA
    • Lavine BK, Davidson CE, Breneman C, Katt W: Analysis of odor structure relationships using electronic Van der Waals surface property descriptors and genetic algorithms. In: Chemometrics and Chemoinformatics. Lavine BK (Ed), American Chemical Society, Washington, DC, USA (2005):127-143.
    • (2005) Chemometrics and Chemoinformatics , pp. 127-143
    • Lavine, B.K.1    Davidson, C.E.2    Breneman, C.3    Katt, W.4
  • 74
    • 0344874154 scopus 로고    scopus 로고
    • A novel fingerprint for the characterization of protein folds
    • Mezei M: A novel fingerprint for the characterization of protein folds. Protein Eng (2003) 16(10):713-715.
    • (2003) Protein Eng , vol.16 , Issue.10 , pp. 713-715
    • Mezei, M.1
  • 75
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk ML, Johnson PL, Church GM: Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 30(5):1255- 1261.
    • (2002) Nucleic Acids Res , vol.30 , Issue.5 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.2    Church, G.M.3
  • 76
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • Benos PV, Bulyk ML, Stormo GD: Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res (2002) 30(20):4442-4451.
    • (2002) Nucleic Acids Res , vol.30 , Issue.20 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 77
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • Benos PV, Lapedes AS, Stormo GD: Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol (2002) 323(4):701-727.
    • (2002) J Mol Biol , vol.323 , Issue.4 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 78
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • Mandel-Gutfreund Y, Margalit H: Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites. Nucleic Acids Res (1998) 26(10):2306-2312.
    • (1998) Nucleic Acids Res , vol.26 , Issue.10 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 79
    • 2342445980 scopus 로고    scopus 로고
    • Modeling within-motif dependence for transcription factor binding site predictions
    • Zhou Q, Liu JS: Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 20(6):909-916.
    • (2004) Bioinformatics , vol.20 , Issue.6 , pp. 909-916
    • Zhou, Q.1    Liu, J.S.2
  • 80
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • Kono H, Sarai A: Structure-based prediction of DNA target sites by regulatory proteins. Proteins (1999) 35(1):114-131.
    • (1999) Proteins , vol.35 , Issue.1 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 81
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe NM, Laskowski RA, Thornton JM: Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res (2001) 29(13):2860-2874.
    • (2001) Nucleic Acids Res , vol.29 , Issue.13 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 82
    • 0028773281 scopus 로고
    • A framework for the DNA-protein recognition code of the probe helix in transcription factors: The chemical and stereochemical rules
    • Suzuki M: A framework for the DNA-protein recognition code of the probe helix in transcription factors: The chemical and stereochemical rules. Structure (1994) 2(4):317-326.
    • (1994) Structure , vol.2 , Issue.4 , pp. 317-326
    • Suzuki, M.1
  • 83
    • 0028609064 scopus 로고
    • DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor and zinc finger families
    • Suzuki M, Yagi N: DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor and zinc finger families. Proc Natl Acad Sci USA (1994) 91(26):12357-12361.
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.26 , pp. 12357-12361
    • Suzuki, M.1    Yagi, N.2
  • 84
    • 0038226895 scopus 로고    scopus 로고
    • DNA sequence and structure: Direct and indirect recognition in protein-DNA binding
    • Steffen NR, Murphy SD, Tolleri L, Hatfield GW, Lathrop RH: DNA sequence and structure: Direct and indirect recognition in protein-DNA binding. Bioinformatics (2002) 18(Suppl 1):S22-S30.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Steffen, N.R.1    Murphy, S.D.2    Tolleri, L.3    Hatfield, G.W.4    Lathrop, R.H.5
  • 85
    • 0028839860 scopus 로고
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
    • Mandel-Gutfreund Y, Schueler O, Margalit H: Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. J Mol Biol (1995) 253(2):370-382.
    • (1995) J Mol Biol , vol.253 , Issue.2 , pp. 370-382
    • Mandel-Gutfreund, Y.1    Schueler, O.2    Margalit, H.3
  • 86
    • 0028046895 scopus 로고
    • Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions
    • Choo Y, Klug A: Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA (1994) 91(23):11168-11172.
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.23 , pp. 11168-11172
    • Choo, Y.1    Klug, A.2
  • 87
    • 0028822256 scopus 로고
    • Consistencies of individual DNA base-amino acid interactions in structures and sequences
    • Lustig B, Jernigan RL: Consistencies of individual DNA base-amino acid interactions in structures and sequences. Nucleic Acids Res (1995) 23(22):4707-4711.
    • (1995) Nucleic Acids Res , vol.23 , Issue.22 , pp. 4707-4711
    • Lustig, B.1    Jernigan, R.L.2
  • 88
    • 27244460904 scopus 로고    scopus 로고
    • Protein-DNA binding specificity predictions with structural models
    • Describes the modeling of the indirect readout of DNA sequences by bound proteins using a simple energy function, •
    • Morozov AV, Havranek JJ, Baker D, Siggia ED: Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 33(18):5781-5798. • Describes the modeling of the indirect readout of DNA sequences by bound proteins using a simple energy function.
    • (2005) Nucleic Acids Res , vol.33 , Issue.18 , pp. 5781-5798
    • Morozov, A.V.1    Havranek, J.J.2    Baker, D.3    Siggia, E.D.4
  • 89
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
    • Pabo C, Nekludova L: Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition? J Mol Biol (2000) 301(3):597-624.
    • (2000) J Mol Biol , vol.301 , Issue.3 , pp. 597-624
    • Pabo, C.1    Nekludova, L.2
  • 90
    • 0024280427 scopus 로고    scopus 로고
    • An ab initio molecular orbital study on the sequence-dependency of DNA conformation: An evaluation of intra- and inter-strand stacking interaction energy
    • Aida M: An ab initio molecular orbital study on the sequence-dependency of DNA conformation: An evaluation of intra- and inter-strand stacking interaction energy. J Theor Biol (1998) 130(3):327-335.
    • (1998) J Theor Biol , vol.130 , Issue.3 , pp. 327-335
    • Aida, M.1
  • 91
    • 0033532946 scopus 로고    scopus 로고
    • Free-energy maps of base-amino acid interactions for DNA-protein recognition
    • Pichierri F, Aida M, Gromiha MM, Sarai A: Free-energy maps of base-amino acid interactions for DNA-protein recognition. J Am Chem Soc (1999) 121(26):6152-6157.
    • (1999) J Am Chem Soc , vol.121 , Issue.26 , pp. 6152-6157
    • Pichierri, F.1    Aida, M.2    Gromiha, M.M.3    Sarai, A.4
  • 92
    • 0034894475 scopus 로고    scopus 로고
    • Liu R, Blackwell TW, States DJ: Conformational model for binding site recognition by the E coli MetJ transcription factor. Bioinformatics (2001) 17(7):622-633.
    • Liu R, Blackwell TW, States DJ: Conformational model for binding site recognition by the E coli MetJ transcription factor. Bioinformatics (2001) 17(7):622-633.
  • 93
    • 33745278855 scopus 로고    scopus 로고
    • Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D: Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006) 441(7093):656-659. • Demonstrates the remarkable increase in activity of an enzyme and recognition site through computational redesign using a physically realistic atomic-level force field.
    • Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D: Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006) 441(7093):656-659. • Demonstrates the remarkable increase in activity of an enzyme and recognition site through computational redesign using a physically realistic atomic-level force field.
  • 94
    • 42449117225 scopus 로고    scopus 로고
    • Sukumar N, Lawrence CE, Breneman CM, Bennett KP, Vitol I: Fuzzy bar code representations of DNA-protein interactions. Division of Computers in Chemistry, 226th American Chemical Society National Meeting, New York, NY, USA (2003):COMP 19.
    • Sukumar N, Lawrence CE, Breneman CM, Bennett KP, Vitol I: Fuzzy bar code representations of DNA-protein interactions. Division of Computers in Chemistry, 226th American Chemical Society National Meeting, New York, NY, USA (2003):COMP 19.
  • 95
    • 42449103111 scopus 로고    scopus 로고
    • Sukumar N, Lawrence CE, Breneman CM, Bennett KP, Vitol I: Dixel modeling of gene expression. Division of Chemical Information, 227th American Chemical Society National Meeting, Anaheim, CA, USA (2004):CINF 1.
    • Sukumar N, Lawrence CE, Breneman CM, Bennett KP, Vitol I: Dixel modeling of gene expression. Division of Chemical Information, 227th American Chemical Society National Meeting, Anaheim, CA, USA (2004):CINF 1.
  • 96
    • 0037341579 scopus 로고    scopus 로고
    • Transferable atom equivalent multi-centered multipole expansion method
    • Whitehead CE, Breneman CM, Sukumar N, Ryan MD: Transferable atom equivalent multi-centered multipole expansion method. J Comput Chem (2003) 24(4):512-529.
    • (2003) J Comput Chem , vol.24 , Issue.4 , pp. 512-529
    • Whitehead, C.E.1    Breneman, C.M.2    Sukumar, N.3    Ryan, M.D.4
  • 97
    • 0036827078 scopus 로고    scopus 로고
    • Prediction of protein retention times in anion-exchange chromatography systems using support vector regression
    • Song M, Breneman CM, Bi J, Sukumar N, Bennett KP, Cramer S, Tugcu N: Prediction of protein retention times in anion-exchange chromatography systems using support vector regression. J Chem Inf Comput Sci (2002) 42(6):1347-1357.
    • (2002) J Chem Inf Comput Sci , vol.42 , Issue.6 , pp. 1347-1357
    • Song, M.1    Breneman, C.M.2    Bi, J.3    Sukumar, N.4    Bennett, K.P.5    Cramer, S.6    Tugcu, N.7
  • 99
    • 42449139822 scopus 로고    scopus 로고
    • Dixel: Sukumar N, Martin JG, Breneman CM, Rensselar Exploratory Center for Cheminformatics Research, Troy, NY, USA (2006). reccr. chem.rpi.edu/Software/Dixel/dixel-index.html
    • Dixel: Sukumar N, Martin JG, Breneman CM, Rensselar Exploratory Center for Cheminformatics Research, Troy, NY, USA (2006). reccr. chem.rpi.edu/Software/Dixel/dixel-index.html
  • 100
    • 37649025842 scopus 로고    scopus 로고
    • Barbano PE, Spivak M, Flajolet M, Nairn AC, Greengard P, Greengard L: A mathematical tool for exploring the dynamics of biological networks. Proc Nat Acad Sci USA (2007) 104(49):19169-19174. • Probes critical points of function in biological networks by using kinetic model parameters as input, and Laplacian eigenvalues for data reduction.
    • Barbano PE, Spivak M, Flajolet M, Nairn AC, Greengard P, Greengard L: A mathematical tool for exploring the dynamics of biological networks. Proc Nat Acad Sci USA (2007) 104(49):19169-19174. • Probes critical points of function in biological networks by using kinetic model parameters as input, and Laplacian eigenvalues for data reduction.
  • 101
    • 35248813000 scopus 로고    scopus 로고
    • Selection of molecules based on shape and electrostatic similarity: Proof of concept of 'electroforms'
    • Jennings A, Tennant M: Selection of molecules based on shape and electrostatic similarity: Proof of concept of 'electroforms'. J Chem Inf Model (2007) 47(5):1829-1838.
    • (2007) J Chem Inf Model , vol.47 , Issue.5 , pp. 1829-1838
    • Jennings, A.1    Tennant, M.2
  • 102
    • 33846881583 scopus 로고    scopus 로고
    • Batista J, Bajorath J: Chemical database mining through entropy-based molecular similarity assessment of randomly generated structural fragment populations. J Chem Inf Model (2007) 47(1):59-68. • Describes a class-independent fragmentation scheme, based on the generation of random molecular fragment populations. This was devised and employed with an information entropy-based molecular similarity metric to search for and identify active molecules. Performance was comparable to similarity searching with 2D fingerprints and multiple active reference structures were reported.
    • Batista J, Bajorath J: Chemical database mining through entropy-based molecular similarity assessment of randomly generated structural fragment populations. J Chem Inf Model (2007) 47(1):59-68. • Describes a class-independent fragmentation scheme, based on the generation of random molecular fragment populations. This was devised and employed with an information entropy-based molecular similarity metric to search for and identify active molecules. Performance was comparable to similarity searching with 2D fingerprints and multiple active reference structures were reported.
  • 103
    • 1042265247 scopus 로고    scopus 로고
    • Approaches to measure chemical similarity - A review
    • Provides an extensive review of molecular similarity measures in the context of QSAR, •
    • Nikolova N, Jaworska J: Approaches to measure chemical similarity - A review. QSAR Comb Sci (2003) 22(9/10):1006-1026. • Provides an extensive review of molecular similarity measures in the context of QSAR.
    • (2003) QSAR Comb Sci , vol.22 , Issue.9-10 , pp. 1006-1026
    • Nikolova, N.1    Jaworska, J.2
  • 104
    • 31544472374 scopus 로고    scopus 로고
    • Using best science in cancer risk assessment
    • Haber L, Maier A, Dourson M: Using best science in cancer risk assessment. Hum Ecol Risk Assess (2006) 12(1):1-8.
    • (2006) Hum Ecol Risk Assess , vol.12 , Issue.1 , pp. 1-8
    • Haber, L.1    Maier, A.2    Dourson, M.3
  • 105
  • 106
    • 0037182165 scopus 로고    scopus 로고
    • Arsenic co-exposure potentiates benzo[a]pyrene genotoxicity
    • Maier A, Schumann BL, Chang X, Talaska G, Puga A: Arsenic co-exposure potentiates benzo[a]pyrene genotoxicity. Mutat Res (2002) 517(1-2):101-111.
    • (2002) Mutat Res , vol.517 , Issue.1-2 , pp. 101-111
    • Maier, A.1    Schumann, B.L.2    Chang, X.3    Talaska, G.4    Puga, A.5
  • 107
    • 0037469988 scopus 로고    scopus 로고
    • Fusion of aroma, FT-IR and UV sensor data based on the Bayesian inference: Application to the discrimination of white grape varieties
    • Roussel S, Bellon-Maurel V, Roger JM, Grenier P: Fusion of aroma, FT-IR and UV sensor data based on the Bayesian inference: Application to the discrimination of white grape varieties. Chemometr Intell Lab Syst (2003) 65(2):209-219.
    • (2003) Chemometr Intell Lab Syst , vol.65 , Issue.2 , pp. 209-219
    • Roussel, S.1    Bellon-Maurel, V.2    Roger, J.M.3    Grenier, P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.