MEGADOCK-Web

MEGADOCK is a high-throughput software tool to predict structure-based protein-protein interactions (PPIs). The MEGADOCK algorithm uses protein-protein docking and a database of 7,528 protein chains and 28,331,628 predicted PPIs from all combinations. Also, the database contains protein structure annotations with chain ID, PDB ID, UniProt AC, KEGG pathway IDs, and known PPI pairs.

Topic

Proteins

Detail

  • Operation: Protein-protein interaction prediction

  • Software interface: Database portal;web user interface;command-line user interface

  • Language: Python;C++;Cuda

  • License: CC BY-NC 4.0

  • Cost: Free

  • Version name: 4.1.1

  • Credit: The Core Research for Evolutional Science and Technology (CREST), the Japan Science and Technology Agency (JST), the Research Complex Program "Wellbeing Research Campus: Creating new values through technological and social innovation" from the Japan Science and Technology Agency (JST), KAKENHI from the Japan Society for the Promotion of Science (JSPS), Platform Project for Supporting Drug Discovery and Life Science Research from Japan Agency for Medical Research and Development (AMED), the Regional Innovation and Ecosystem Formation Program "Program to Industrialize an Innovative Middle Molecule Drug Discovery Flow through Fusion of Computational Drug Design and Chemical Synthesis Technology" from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT), Leave a Nest, Co., Ltd., Microsoft Japan, Co., Ltd.

  • Input: -

  • Output: -

  • Contact: Masahito Ohue ohue@c.titech.ac.jp, Yutaka Akiyama akiyama@c.titech.ac.jp

  • Collection: -

  • Maturity: Mature

Publications

  • MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.
  • Ohue M, Shimoda T, Suzuki S, Matsuzaki Y, Ishida T, Akiyama Y. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinformatics. 2014 Nov 15;30(22):3281-3. doi: 10.1093/bioinformatics/btu532. Epub 2014 Aug 6. PMID: 25100686; PMCID: PMC4221127.
  • https://doi.org/10.1093/bioinformatics/btu532
  • PMID: 25100686
  • PMC: PMC4221127
  • MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.
  • Hayashi T, et al. MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. 2018; 19:62. doi: 10.1186/s12859-018-2073-x
  • https://doi.org/10.1186/s12859-018-2073-x
  • PMID: 29745830
  • PMC: PMC5998897
  • MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.
  • Ohue M, Matsuzaki Y, Uchikoga N, Ishida T, Akiyama Y. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data. Protein Pept Lett. 2014;21(8):766-78. doi: 10.2174/09298665113209990050. PMID: 23855673; PMCID: PMC4443796.
  • https://doi.org/10.2174/09298665113209990050
  • PMID: 23855673
  • PMC: PMC4443796

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