BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

154 related articles for article (PubMed ID: 25100686)

  • 1. 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
    Bioinformatics; 2014 Nov; 30(22):3281-3. PubMed ID: 25100686
    [TBL] [Abstract][Full Text] [Related]  

  • 2. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.
    Ohue M; Matsuzaki Y; Uchikoga N; Ishida T; Akiyama Y
    Protein Pept Lett; 2014; 21(8):766-78. PubMed ID: 23855673
    [TBL] [Abstract][Full Text] [Related]  

  • 3. MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.
    Hayashi T; Matsuzaki Y; Yanagisawa K; Ohue M; Akiyama Y
    BMC Bioinformatics; 2018 May; 19(Suppl 4):62. PubMed ID: 29745830
    [TBL] [Abstract][Full Text] [Related]  

  • 4. MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.
    Matsuzaki Y; Uchikoga N; Ohue M; Shimoda T; Sato T; Ishida T; Akiyama Y
    Source Code Biol Med; 2013 Sep; 8(1):18. PubMed ID: 24004986
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Spresso: an ultrafast compound pre-screening method based on compound decomposition.
    Yanagisawa K; Komine S; Suzuki SD; Ohue M; Ishida T; Akiyama Y
    Bioinformatics; 2017 Dec; 33(23):3836-3843. PubMed ID: 28369284
    [TBL] [Abstract][Full Text] [Related]  

  • 6. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.
    Jiménez-García B; Pons C; Fernández-Recio J
    Bioinformatics; 2013 Jul; 29(13):1698-9. PubMed ID: 23661696
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Cell-Dock: high-performance protein-protein docking.
    Pons C; Jiménez-González D; González-Álvarez C; Servat H; Cabrera-Benítez D; Aguilar X; Fernández-Recio J
    Bioinformatics; 2012 Sep; 28(18):2394-6. PubMed ID: 22815362
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Protein-protein interaction specificity is captured by contact preferences and interface composition.
    Nadalin F; Carbone A
    Bioinformatics; 2018 Feb; 34(3):459-468. PubMed ID: 29028884
    [TBL] [Abstract][Full Text] [Related]  

  • 9. ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.
    Porter KA; Xia B; Beglov D; Bohnuud T; Alam N; Schueler-Furman O; Kozakov D
    Bioinformatics; 2017 Oct; 33(20):3299-3301. PubMed ID: 28430871
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Faster sequence homology searches by clustering subsequences.
    Suzuki S; Kakuta M; Ishida T; Akiyama Y
    Bioinformatics; 2015 Apr; 31(8):1183-90. PubMed ID: 25432166
    [TBL] [Abstract][Full Text] [Related]  

  • 11. CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts.
    Chermak E; Petta A; Serra L; Vangone A; Scarano V; Cavallo L; Oliva R
    Bioinformatics; 2015 May; 31(9):1481-3. PubMed ID: 25535242
    [TBL] [Abstract][Full Text] [Related]  

  • 12. MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory.
    Ohue M
    BMC Res Notes; 2023 Sep; 16(1):229. PubMed ID: 37737185
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Accounting for pairwise distance restraints in FFT-based protein-protein docking.
    Xia B; Vajda S; Kozakov D
    Bioinformatics; 2016 Nov; 32(21):3342-3344. PubMed ID: 27357172
    [TBL] [Abstract][Full Text] [Related]  

  • 14. NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID.
    Gaudreault F; Morency LP; Najmanovich RJ
    Bioinformatics; 2015 Dec; 31(23):3856-8. PubMed ID: 26249810
    [TBL] [Abstract][Full Text] [Related]  

  • 15. IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
    Moal IH; Barradas-Bautista D; Jiménez-García B; Torchala M; van der Velde A; Vreven T; Weng Z; Bates PA; Fernández-Recio J
    Bioinformatics; 2017 Jun; 33(12):1806-1813. PubMed ID: 28200016
    [TBL] [Abstract][Full Text] [Related]  

  • 16. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution.
    Andreani J; Faure G; Guerois R
    Bioinformatics; 2013 Jul; 29(14):1742-9. PubMed ID: 23652426
    [TBL] [Abstract][Full Text] [Related]  

  • 17. pyDockSAXS: protein-protein complex structure by SAXS and computational docking.
    Jiménez-García B; Pons C; Svergun DI; Bernadó P; Fernández-Recio J
    Nucleic Acids Res; 2015 Jul; 43(W1):W356-61. PubMed ID: 25897115
    [TBL] [Abstract][Full Text] [Related]  

  • 18. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers.
    Pierce BG; Wiehe K; Hwang H; Kim BH; Vreven T; Weng Z
    Bioinformatics; 2014 Jun; 30(12):1771-3. PubMed ID: 24532726
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Building a virtual ligand screening pipeline using free software: a survey.
    Glaab E
    Brief Bioinform; 2016 Mar; 17(2):352-66. PubMed ID: 26094053
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem.
    Ban T; Ohue M; Akiyama Y
    Comput Biol Chem; 2018 Apr; 73():139-146. PubMed ID: 29482137
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.