title: Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target.
abstract: A search of broader range of chemical space is important for drug discovery. Different methods of computer-aided drug discovery (CADD) are known to propose compounds in different chemical spaces as hit molecules for the same target protein. This study aimed at using multiple CADD methods through open innovation to achieve a level of hit molecule diversity that is not achievable with any particular single method. We held a compound proposal contest, in which multiple research groups participated and predicted inhibitors of tyrosine-protein kinase Yes. This showed whether collective knowledge based on individual approaches helped to obtain hit compounds from a broad range of chemical space and whether the contest-based approach was effective.
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.
authors.forename: Shuntaro
authors.initials: S
authors.lastname: Chiba
authors.affiliation: Level Five Co. Ltd., Shiodome Shibarikyu Bldg., 1-2-3 Kaigan, Minato-ku, Tokyo 105-0022, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Ikeda
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.|Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Ishida
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India.
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
authors.affiliation: Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan.
authors.forename: Y-H
authors.initials: YH
authors.lastname: Taguchi
authors.affiliation: Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan.
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Iwadate
authors.affiliation: Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Umeyama
authors.affiliation: Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495 Japan.
authors.forename: Kun-Yi
authors.initials: KY
authors.lastname: Hsin
authors.affiliation: Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495 Japan.|The Systems Biology Research Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Minato-ku, Tokyo 108-0071 Japan.|Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
authors.affiliation: Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Yamamoto
authors.affiliation: PharmaDesign Inc., 2-19-8, Hatchobori, Chuo-ku, Tokyo 104-0032 Japan.
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Sugaya
authors.affiliation: Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa, Nagoya 464-8603, Japan.
authors.forename: Koya
authors.initials: K
authors.lastname: Kato
authors.affiliation: Division of Neurogenetics, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Okuno
authors.affiliation: Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa, Nagoya 464-8603, Japan.
authors.forename: George
authors.initials: G
authors.lastname: Chikenji
authors.affiliation: Information and Mathematical Science and Bioinformatics Co., Ltd., Level 6 OWL TOWER, 4-21-1 Higashi-Ikebukuro, Toshima-ku, Tokyo 170-0013 Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Mochizuki
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.|Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Yasuo
authors.affiliation: Global Scientific Information and Computing Center, Tokyo Institute of Technology 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.|Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Nunkyo-ku, Tokyo, 113-8657.
authors.forename: Ryunosuke
authors.initials: R
authors.lastname: Yoshino
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.|Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Yanagisawa
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.|Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Ban
authors.affiliation: Forerunner Pharma Research, Co., Ltd., Yokohama Bio Industry Center, 1-6 Shuehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan.
authors.forename: Reiji
authors.initials: R
authors.lastname: Teramoto
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India.
authors.forename: Chandrasekaran
authors.initials: C
authors.lastname: Ramakrishnan
authors.affiliation: Centre of Advanced Study in Crystallography and Biophysics and Bioinformatics Infrastructure Facility (DBT Funded), University of Madras, Chennai 600025, Tamilnadu, India.
authors.forename: A Mary
authors.initials: AM
authors.lastname: Thangakani
authors.affiliation: Centre of Advanced Study in Crystallography and Biophysics and Bioinformatics Infrastructure Facility (DBT Funded), University of Madras, Chennai 600025, Tamilnadu, India.
authors.forename: D
authors.initials: D
authors.lastname: Velmurugan
authors.affiliation: National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085 Japan.
authors.forename: Philip
authors.initials: P
authors.lastname: Prathipati
authors.affiliation: National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085 Japan.
authors.forename: Junichi
authors.initials: J
authors.lastname: Ito
authors.affiliation: National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085 Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Tsuchiya
authors.affiliation: National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085 Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
authors.affiliation: Center for Life Science Technologies, RIKEN, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe-shi, Hyogo 650-0047 Japan.
authors.forename: Teruki
authors.initials: T
authors.lastname: Honma
authors.affiliation: Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo 105-0003 Japan.
authors.forename: Takatsugu
authors.initials: T
authors.lastname: Hirokawa
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.|Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.|Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo 105-0003 Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501 Japan.|Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.|Global Scientific Information and Computing Center, Tokyo Institute of Technology 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550 Japan.|Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo 105-0003 Japan.
authors.forename: Masakazu
authors.initials: M
authors.lastname: Sekijima
mesh_terms: D004353:Drug Evaluation, Preclinical; D006801:Humans; D025341:Principal Component Analysis; D047428:Protein Kinase Inhibitors / Q000032:analysis* / Q000494:pharmacology*; D051575:Proto-Oncogene Proteins c-yes / Q000037:antagonists & inhibitors* / Q000737:chemistry; D015203:Reproducibility of Results; D019061:src-Family Kinases / Q000378:metabolism
chemical_list: D047428:Protein Kinase Inhibitors; D051575:Proto-Oncogene Proteins c-yes; C489834:YES1 protein, human; D019061:src-Family Kinases