Publications (Yoshimasa Takahashi)

Original Articles

1)     Molecular Evolutionary Algorithm for Structure Design and Structure Generation, Kentaro Kawai, Kazutaka Yoshimaru, Yoshimasa Takahashi,  J. Comput. Chem. Jpn., 10,25-31(2011). <Japanese>

2)     Virtual Screening of Antihypertensive Drugs Using Support Vector Machines, Kentaro Kawai, Yoshimasa Takahashi, J. Comput. Chem. Jpn., 9,167-176(2010). <Japanese>

3)     Identification of the Dual Action Antihypertensive Drugs Using TFS-Based Support Vector Machines, Kentaro Kawai, Yoshimasa Takahashi, Chem-Bio Informatics Journal, 9, 41-51 (2009).

4)     Classification and Prediction of Multiple Drug Actions using SVM,  Yoshimasa Takahashi, Kentaro Kawai, Seibutsu-kogaku Kaishi, 86(12), 589-592 (2008). <Japanese>

5)     "Predictive Activity Profiling of Drugs by Topological-Fragment-Spectra-Based Support Vector Machines", Kentaro Kawai, Satoshi Fujishima, and Yoshimasa Takahashi, J. Chem. Inf. Model., 48, 1152-1160 (2008).

6)     Pharmacophore Refinement in the Chemical Structure Space, Satoshi Fujishima, Yoshimasa Takahashi, and Takashi Okada, J. Comput. Chem. Jpn., 7, 63-70 (2008).

7)     Mining of Three-Dimensional Structural Fragments in Drug Molecules, Hiroaki Kato, Takashi Koshika, Yoshimasa Takahashi, and Hidetsugu Abe, New Frontiers in Artificial Intelligence, LNAI 3609, Springer-Verlag, pp.538-545 (2007).

8)     Pharmacophore Knowlede Refinement in the Chemical Structure Space, S. Fujishima, Y. Takahashi, T. Okada, Discovery Science 2007, LNAI 4755, Springer-Verlag, pp.243-247(2007).

9)     Extended Study of the Classification of Dopamine Receptor Agonists and Antagonists using a TFS-based Support Vector Machine, S. Fujishima, Y. Takahashi, K. Nishikoori, H. Kato, and T. Okada, New Generation Computing, 25 203-212 (2007).

10)  New Molecular Fragmental Descriptors and Their Application to the Prediction of Fish Toxicity, S. Alikhanidi and Y. Takahashi, MATCH, 55, 205-232 (2006)

11)  Three-Dimensional Protein Structural Data Mining Based on Clycine Filter Reduced Representation, H. Kato, S. Chikamatsu, Y. Takahashi, H. Abe, J. Comput. Chem. Jpn., 4, 33-42 (2005). <Japanese>

12)  Identification of dopamine D1 receptor agonists and antagonists under existing noise compounds by TFS-based ANN and SVM, Y. Takahashi, S. Fujishima, K. Nishikoori, H. Kato, and T. Okada, J. Comput. Chem. Jpn., 4, 43-48 (2005).

13)  Discovery of Risk Chemicals by Active Mining, T. Okada and Y. Takahashi, Journal of Japanese Society of Artificial Intelligence, 20, 211-218(2005) <Japanese>

14)  Classification of Pharmacological Activity of Drugs Using Support Vector Machine, Y. Takahashi, K. Nishikoori and S. Fujishima, LNCS 3430, pp.303-311 , Springer-Verlag, 2005

15)  Chemical data mining based on non-terminal vertex graph, Y. Takahashi, Systems, Man and Cybernetics, 2004 IEEE International Conference, Volume 5,  2004 pp. 4583 – 4587.

16)  Development of Software Tools to Construct a 3D Motif Dictionary of Proteins, H. Kato, H. Miyata, N. Uchimura, Y. Takahashi, H. Abe, J. Comput. Chem. Jpn., 3, 137-144 (2004). <Japanese>

17)  Protein Classification Using Comparative Molecular Interaction Profile Analysis System, Y. Hayashi, M. Kobayashi, K. Sakaguchi, N. Iwata, M. Kobayashi, Y. Kikuchi and Y. Takahashi, J. Bioinf. Comput. Biol., 2, 497-510 (2004).

18)  Classification and Prediction of Drug Actions by Machine Learning, Yoshimasa Takahashi, Katsumi Nishikori, Satoshi Fujishima, SAR News, No.6, pp.10-13(2004). <Japanese>

19)  Classification of Dopamine Antagonists using TFS-Based Artificial Neural Network, S. Fujishima, Y. Takahashi, J. Chem. Inf. Comput. Sci., 44, 1006-1009 (2004).

20)  Pesticide Persistence in Environment - Collected Data and Structure-based Analysis, S. Alikhanidi and Y. Takahashi, J. Comput. Chem. Jpn., 3, 59-70 (2004).

21)  Topological Fragment Spectra (TFS) Peak Identification System for Chemical Structure Data Mining, S. Fujishima, Y. Takahashi, J. Comput. Chem. Jpn., 3, 49-58 (2004).  <Japanese>

22)  Chemical Data Mining Based on Structural Similarity, Y. Takahashi, S. Fujishima, H. Kato, J. Comput. Chem. Jpn., 2, 119-126 (2003). <Japanese>

23)  MolSpace: A Computer Desktop Tool for Visualization of Massive Molecular Data, Y. Takahashi, M. Konji, S. Fujishima, J. Mol. Graph. Model., 21, 333-339(2003)

24)  Construction of a Three-Dimensional Motif Dictionary for Protein Structural Data Mining, H. Kato, T. Tadokoro, H. Miyata, S. Chikamatsu, Y. Takahashi, H. Abe, Transaction of the Japanese Society for Artificial Intelligence, 17, 608-613(2002). <Japanese>

25)  Artificial Neural Network for the Toxicity Prediction of Organic Molecules, G. Admans, Y. Takahashi, S. Ban, H. Kato, H. Abe and S. Hanai, Bull Chem. Soc. Jpn.,74,2451-2461 (2001).

26)  Automated identification of three-dimensional common structural features of proteins., H.Kato and Y.Takahashi, J. Chem. Soft., 7, 161-170 (2001).

27)  Structural Similarity Analysis Based on Topological Fragment Spectra, Y.Takahashi, H.Ohoka, Y.Ishiyama, Advances in Molecular Similarity, 2, 93-104(1998)

28)  SS3D-P2: Three-dimensional Substructure Search Program for Protein Motifs Based on Secondary Structure Elements, H. Kato and Y. Takahashi, Comput. Appl. Biol. Sci., 13, 593-600(1997).

29)  Three-dimensional Structural Feature Search of Proteins, H. Kato and Y. Takahashi,  Bull. Chem. Soc. Jpn., 70, 1523-1529(1997).

30)  Development of A Three-Dimensional Substructure Search for Organic Molecules, H. Kato, Y. Takahashi, Bull. Chem. Soc. Jpn., 70, 123-127(1997)

31)  Exhaustive Conformational Searches for Superimposition of Acaricidal Compounds, T. Akagi, Y.Takahashi, S.Sasaki, Quant.Struc.Act.Relat., 15, 290-295(1996).

32)  Computational Algorithm Management in A Global Networked Context, W.D.Ihlenfeldt, Y.Takahashi, H.Abe, AIP Proc. 330, 520-525(1995).

33)  Data Flow Processing for Computational Chemistry problems, W.D.Ihlenfeldt, Y.Takahashi, H.Abe, AIP Proc., 330, 514-519(1995).

34)  Identification of Structural Similarity of Organic Molecules, Y.Takahashi, Topics Curr. Chem., 174, 106-133(1995).

35)  Evaluation of Molecular Similarity Using Topological Fragment Spectra, Y.Takahashi, Y.Ishiyama, Molecular Similarity and Reactivity, R.Carbo (Ed), Kluwer Academic Publishers, 1995, pp 311-316.

36)  - Conformational Pattern Clustering of Protein Amino Acid Residues Using The Potential Function Method, M.Kamimura, Y.Takahashi, Comput. Appl. Bio. Sci., 10, 163-169(1994).

37)  36)     Computation and Management of Chemical Properties in CACTVS: An Extensible Networked Approach toward Modularity and Compatibility, W.D.Ihlenfeldt, Y.Takahashi, H.Abe, S.Sasaki,   J. Chem. Inf. Comput. Sci., 34, 109-116(1994).

38)  Automatic Extraction of Ring Substructures from a Chemical Structure, Y.Takahashi, J. Chem.  Inf. Comput. Sci., 34, 167-170(1994).

39)  Automatic Identification and Manipulation of Receptor Sites in Proteins. 2. Electrostatic Complementarity Analysis for the Evaluation and Selection of Candidate Ligand Receptor Sites,  C.A. DelCarpio, Y.Takahashi, S. Sasaki, J. Chem. Inf. Comput. Sci., 33, 769-775(1993).

40)  A New Approach to the Automatic Identification of Candidates for Ligand Receptor Sites in Proteins: (I)Search for Pocket Regions, C.A.Del Carpio, Y.Takahashi, S.Sasaki, J. Mol. Graphics., 11, 23-29(1993).

41)  Automatic Identification of Receptor Sites in Proteins.  Electrophysical Analysis of Ligand-Receptor Interactions, C.A.Del Carpio, Y.Takahashi, S.Sasaki, Computer Aided Innovation of New Materials II, 1993, Elsevier Science Publishers B.V., pp.1151-1154.

42)  Algorithm Development in Chemistry: The Detection of Common Three-Dimensional Substructures in Large Sets of Possibly Flexible Molecules, W.D.Ihlenfeldt, Y.Takahashi, H.Abe, S.Sasaki, Computer Aided Innovation of New Materials II, 1993, Elsevier Science Publishers B.V., pp.1155-1158.

43)  - Conformational Pattern Clustering of Protein Amino Acid Residues Using Potential Function Method, M.Kamimura, Y.Takahashi, S.Sasaki, J. Protein Chem., 11, 393-394(1992).

44)  Automatic Identification of Molecular Similarity Using Reduced-Graph Representation of Chemical Structure, Y.Takahashi, M.Sukekawa S.Sasaki, J. Chem .Inf.Comput. Sci., 32, 639-643(1992).

45)  The Relationship between Anesthetic Potency (Minimum Alveolar Concentration) and Molecular Shape; Structural Studies on Conventional Inhalational Anesthetics, Y.Shiraishi, H.Fujise, K.Ikeda, Y.Takahashi, T.Akagi, S.Sasaki, Y. Nozue, J. Anesthesia, 5, 370-379(1991).

46)  Automatic Recognitin of Common Structural Features Among Chemical Compounds Using Reduced Structure Representation Based on Functional Groups, Y. Takahashi, M. Sukekawa and S. Sasaki, Computer Aided Innovation of New Materials, 1991, pp.433-438, Elsevier Science Publishers B.V.(North-Holland).

47)  Systematization of Semantic Descriptions of Odors, H.Abe, S.Kanaya, T.Komukai, Y.Takahashi, S.Sasaki, Anal. Chim. Acta, 239, 73-85(1990).

48)  Three-Dimensional Pharmacophoric Pattern Search Using COMPASS : Nootropic Agents, Y.Takahashi, T.Akagi, S.Sasaki, Tetrahedron Comput. Method., 3, 7-35(1990).

49)  Method for Monitoring Sensor Stability in a Multiple Semiconductor Gas-Sensor System, H.Abe, S.Kanaya, Y.Takahashi, S.Sasaki, Anal. Chim. Acta, 225, 89-96(1989).

50)  Combined Semiconductor Gas Sensor System for Detection of Specific Substances in Particular Environments, H.Abe, S.Kanaya, Y.Takahashi, S.Sasaki, Anal. Chim. Acta, 219, 213-222(1989).

51)  A new System, TUTORS, for Computer-Aided Molecular Design, Y.Takahashi, K.Hosokawa, F.Yoshida, M.Ozaki, S.Sasaki, Anal. Chim. Acta, 217, 61-83(1989).

52)  Total System of Molecular Design, S.Sasaki, Y.Takahashi, K.Funatsu, Physical Property Prediction in Organic Chemistry (Eds. C. Jochum, M.G. Hicks, J. Sunkel) 1988, pp.255-301.

53)  Extended Studies of The Automated Odor-Sensing System Based on Plural Semiconductor Gas Sensors with Computerized Pattern Recognition Techniques, H.Abe, S.Kanaya, Y.Takahashi, S.Sasaki, Anal. Chim. Acta, 215, 155-162(1988).

54)  Structure-Activity Study of Systemic Acaricidal N-Substituted Chloromethanesulfonamides by the ORMUCS Method, M.Tamaru, H.Ogawa, T.Nishimura, Y.Takahashi, S.Sasaki, J. Pesticide Sci., 13, 1-6(1988).

55)  Automated Recognition of Common Structural Patterns among Drug Molecules, Yoshimasa Takahashi, Shin-ichi Sasaki, J. Synthetic Organic Chemistry, Japan, 45, 1087-1097(1987). <Japanese>

56)  Automated Recognition of Common Geometrical Pattern among a Variety of Three-Dimensional Molecular Structures, Y.Takahashi, S.Maeda, S.Sasaki, Anal. Chim. Acta, 200, 363-377(1987).

57)  Automated Odor-Sensing System Based on Plural Semiconductor Gas Sensors and Computerized Pattern Recognition Techniques, H.Abe, T.Yoshimura, S.Kanaya, Y.Takahashi, Y.Miyashita, S.Sasaki, Anal. Chim. Acta, 194, 1-9(1987).

58)  Application of ORMUCS Method to Structure-Activity Studies on Fungicidal Activity of Mepronil Derivatives, Y.Takahashi, M.Tamaru, I.Shimazaki, S.Ito, S.Kawada, Y.Suda, S.Sasaki, Quant. Struct.-Act. Relat. 6, 17-21(1987).

59)  Recognition of Largest Common Structural Fragment among a Variety of  Chemical Structures, Y.Takahashi, Y.Satoh, H.Suzuki, S.Sasaki, Anal. Sci., 3, 23-28(1987).

60)  Structure-Activity Relationships and Drug Design by Computer, Y. Takahashi, S. Sasaki, Fine Chemical, 15, 48-58(1986). <Japanese>

61)  Computer-Assisted Structure-Taste Studies on Sulfamates by Pattern Recognition Methods, Y.Miyashita, Y.Takahashi, C.Takayama, T.Ohkubo, K.Funatsu, S.Sasaki, Anal. Chim. Acta, 184, 143-149(1986).

62)  Application of Pattern Recognition Techniques to Assessment of Hazards of Chemical Substances, S.Sasaki, Y.Takahashi, Hazard Assess.Chem.,  5, 61-101(1986).

63)  Enumeration of Unique Substructure from a Chemical Structure, Y.Takahashi, Y.Satoh, H. Suzuki, H.Abe, S.Sasaki, Anal. Sci., 2, 321-323(1986).

64)  Structure-Taste Correlation of L-Aspartyl Dipeptides using SIMCA Method Y.Miyashita, Y.Takahashi, C.Takayama, K.Sumi, K.Nakatsuka, T.Ohkubo,@H.Abe, S.Sasaki, J. Med. Chem., 29, 906-912(1986).

65)  Discriminative Structural Analysis Using Pattern Recognition Techniques in the Structure-Taste Problem of Perillartines, Y.Takahashi, Y.Miyashita, Y.Tanaka, H.Hayasaka, H.Abe, S.Sasaki, J. Pham. Sci., 73, 737-741(1984).

66)  A New Approach for Ordered Multicategorical Classification Using Simplex Technique, Y.Takahashi, Y.Miyashita, H.Abe, S.Sasaki, Bunseki Kagaku, 33, E487-494(1984).

67)  Computer-Assisted Structure-Carcinogenicity Studies on Polynuclear Aromatic Hydrocarbons by Pattern Recognition Methods: The role of the Bay and L-Regions, Y.Miyashita, Y.Takahashi, S.Daiba, H.Abe, S.Sasaki, Anal. Chim. Acta, 143, 35-44(1982).

68)  A Consideration for Structure-Taste Correlations of Perillartines Using Pattern@Recognition Techniques, Y.Takahashi, Y.Miyashita, Y.Tanaka,@H.Abe, S.Sasaki, J. Med. Chem., 25, 1245-1248(1982).

69)  Application of Pattern Recognition to Structure-Activity Problems Use of minimal spanning tree, Y.Miyashita, Y.Takahashi, Y.Yotsui, H.Abe, S.Sasaki, Anal.  Chim. Acta, 133, 615-624(1981).

70)  Computer-Assisted Structure-Carcinogenicity Studies on Polycyclic Aromatic Hydrocarbons by Pattern Recognition Methods, Y.Miyashita, T.Seki, Y.Takahashi, S.Daiba, Y.Tanaka, Y.Yotsui, H.Abe, S.Sasaki, Anal. Chim. Acta, 133, 603-613(1981).

71)  The Use of Cluster Analysis and Display Method of Pattern Recognition in Structure-Activity Studies of Antibiotics, Y.Miyashita, Y.Takahashi, Y.Yotsui, H.Abe, S.Sasaki, CODATA Bull., No.41, 37-41(1981).

72)  A Structure-Biological Activity Study Based on Cluster Analysis and The Nonlinear Mapping Method of Pattern Recognition, Y.Takahashi, Y.Miyashita,@H.Abe, S.Sasaki, Y.Yotsui M.Sano,@Anal. Chim. Acta, 122, 241-247(1980).

73)  Successive Extraction of Koshu White Wine for Fraction of  Flavonoid Polymers, K.Yokotsuka, Y.Takahashi, M.Yoshii, T.Kushida, J. Ferment. Technol., 56, 121-127(1978).