title: systemsDock: a web server for network pharmacology-based prediction and analysis.
abstract: We present systemsDock, a web server for network pharmacology-based prediction and analysis, which permits docking simulation and molecular pathway map for comprehensive characterization of ligand selectivity and interpretation of ligand action on a complex molecular network. It incorporates an elaborately designed scoring function for molecular docking to assess protein-ligand binding potential. For large-scale screening and ease of investigation, systemsDock has a user-friendly GUI interface for molecule preparation, parameter specification and result inspection. Ligand binding potentials against individual proteins can be directly displayed on an uploaded molecular interaction map, allowing users to systemically investigate network-dependent effects of a drug or drug candidate. A case study is given to demonstrate how systemsDock can be used to discover a test compound's multi-target activity. systemsDock is freely accessible at http://systemsdock.unit.oist.jp/.
authors.affiliation: Integrated Open Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0412, Japan kunyi.hsin@oist.jp.
authors.forename: Kun-Yi
authors.initials: KY
authors.lastname: Hsin
authors.affiliation: The Systems Biology Institute, Minato, Tokyo 108-0071, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Matsuoka
authors.affiliation: Integrated Open Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0412, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Asai
authors.affiliation: Integrated Open Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0412, Japan.
authors.forename: Kyota
authors.initials: K
authors.lastname: Kamiyoshi
authors.affiliation: Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Minato, Tokyo 108-8639, Japan.
authors.forename: Tokiko
authors.initials: T
authors.lastname: Watanabe
authors.affiliation: Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Minato, Tokyo 108-8639, Japan Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53711, USA.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kawaoka
authors.affiliation: Integrated Open Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0412, Japan The Systems Biology Institute, Minato, Tokyo 108-0071, Japan Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa 230-0045, Japan kitano@sbi.jp.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
mesh_terms: D000146:Acids, Carbocyclic; D003517:Cyclopentanes / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D006146:Guanidines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D006801:Humans; D007251:Influenza, Human / Q000378:metabolism / Q000821:virology; D020407:Internet; D008024:Ligands; D062105:Molecular Docking Simulation; D009975:Orthomyxoviridae / Q000187:drug effects / Q000378:metabolism; D053139:Oseltamivir / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D010600:Pharmacology / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D000146:Acids, Carbocyclic; D003517:Cyclopentanes; D006146:Guanidines; D008024:Ligands; D053139:Oseltamivir; C414210:peramivir