BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

205 related articles for article (PubMed ID: 35580866)

  • 1. fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation.
    Wang Z; Pan H; Sun H; Kang Y; Liu H; Cao D; Hou T
    Brief Bioinform; 2022 Sep; 23(5):. PubMed ID: 35580866
    [TBL] [Abstract][Full Text] [Related]  

  • 2. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.
    Wang Z; Wang X; Li Y; Lei T; Wang E; Li D; Kang Y; Zhu F; Hou T
    Bioinformatics; 2019 May; 35(10):1777-1779. PubMed ID: 30329012
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening.
    Yang M; Bo Z; Xu T; Xu B; Wang D; Zheng H
    Brief Bioinform; 2023 Jul; 24(4):. PubMed ID: 37328705
    [TBL] [Abstract][Full Text] [Related]  

  • 4. HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
    Weng G; Wang E; Wang Z; Liu H; Zhu F; Li D; Hou T
    Nucleic Acids Res; 2019 Jul; 47(W1):W322-W330. PubMed ID: 31106357
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Postprocessing of docked protein-ligand complexes using implicit solvation models.
    Lindström A; Edvinsson L; Johansson A; Andersson CD; Andersson IE; Raubacher F; Linusson A
    J Chem Inf Model; 2011 Feb; 51(2):267-82. PubMed ID: 21309544
    [TBL] [Abstract][Full Text] [Related]  

  • 6. istar: a web platform for large-scale protein-ligand docking.
    Li H; Leung KS; Ballester PJ; Wong MH
    PLoS One; 2014; 9(1):e85678. PubMed ID: 24475049
    [TBL] [Abstract][Full Text] [Related]  

  • 7. CB-Dock: a web server for cavity detection-guided protein-ligand blind docking.
    Liu Y; Grimm M; Dai WT; Hou MC; Xiao ZX; Cao Y
    Acta Pharmacol Sin; 2020 Jan; 41(1):138-144. PubMed ID: 31263275
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity.
    Nguyen NT; Nguyen TH; Pham TNH; Huy NT; Bay MV; Pham MQ; Nam PC; Vu VV; Ngo ST
    J Chem Inf Model; 2020 Jan; 60(1):204-211. PubMed ID: 31887035
    [TBL] [Abstract][Full Text] [Related]  

  • 9. MM-GB/SA rescoring of docking poses in structure-based lead optimization.
    Guimarães CR; Cardozo M
    J Chem Inf Model; 2008 May; 48(5):958-70. PubMed ID: 18422307
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking.
    Agarwal R; T RR; Smith JC
    J Chem Inf Model; 2023 Dec; 63(23):7444-7452. PubMed ID: 37972310
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Cross-docking benchmark for automated pose and ranking prediction of ligand binding.
    Wierbowski SD; Wingert BM; Zheng J; Camacho CJ
    Protein Sci; 2020 Jan; 29(1):298-305. PubMed ID: 31721338
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA.
    Dickerhoff J; Warnecke KR; Wang K; Deng N; Yang D
    Int J Mol Sci; 2021 Oct; 22(19):. PubMed ID: 34639142
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function.
    Wang Z; Zheng L; Wang S; Lin M; Wang Z; Kong AW; Mu Y; Wei Y; Li W
    Brief Bioinform; 2023 Jan; 24(1):. PubMed ID: 36502369
    [TBL] [Abstract][Full Text] [Related]  

  • 14. MDockPeP: A Web Server for Blind Prediction of Protein-Peptide Complex Structures.
    Xu X; Zou X
    Methods Mol Biol; 2020; 2165():259-272. PubMed ID: 32621230
    [TBL] [Abstract][Full Text] [Related]  

  • 15. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm.
    Chang DT; Oyang YJ; Lin JH
    Nucleic Acids Res; 2005 Jul; 33(Web Server issue):W233-8. PubMed ID: 15991337
    [TBL] [Abstract][Full Text] [Related]  

  • 16. DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening.
    Zhang H; Zhang T; Saravanan KM; Liao L; Wu H; Zhang H; Zhang H; Pan Y; Wu X; Wei Y
    Methods; 2022 Sep; 205():247-262. PubMed ID: 35878751
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.
    Wang Z; Sun H; Yao X; Li D; Xu L; Li Y; Tian S; Hou T
    Phys Chem Chem Phys; 2016 May; 18(18):12964-75. PubMed ID: 27108770
    [TBL] [Abstract][Full Text] [Related]  

  • 18. ATPdock: a template-based method for ATP-specific protein-ligand docking.
    Rao L; Jia NX; Hu J; Yu DJ; Zhang GJ
    Bioinformatics; 2022 Jan; 38(2):556-558. PubMed ID: 34546290
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation.
    Grudinin S; Kadukova M; Eisenbarth A; Marillet S; Cazals F
    J Comput Aided Mol Des; 2016 Sep; 30(9):791-804. PubMed ID: 27718029
    [TBL] [Abstract][Full Text] [Related]  

  • 20. MM/PB(GB)SA benchmarks on soluble proteins and membrane proteins.
    Wang S; Sun X; Cui W; Yuan S
    Front Pharmacol; 2022; 13():1018351. PubMed ID: 36532746
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.