BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

189 related articles for article (PubMed ID: 23548025)

  • 1. Artificial neural networks for efficient clustering of conformational ensembles and their potential for medicinal chemistry.
    Pandini A; Fraccalvieri D; Bonati L
    Curr Top Med Chem; 2013; 13(5):642-51. PubMed ID: 23548025
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Conformational and functional analysis of molecular dynamics trajectories by self-organising maps.
    Fraccalvieri D; Pandini A; Stella F; Bonati L
    BMC Bioinformatics; 2011 May; 12():158. PubMed ID: 21569575
    [TBL] [Abstract][Full Text] [Related]  

  • 3. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.
    De Paris R; Quevedo CV; Ruiz DD; Norberto de Souza O
    PLoS One; 2015; 10(7):e0133172. PubMed ID: 26218832
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis.
    Yao XQ; Hamelberg D
    Acc Chem Res; 2019 Dec; 52(12):3455-3464. PubMed ID: 31793290
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.
    Fraccalvieri D; Tiberti M; Pandini A; Bonati L; Papaleo E
    Mol Biosyst; 2012 Oct; 8(10):2680-91. PubMed ID: 22802143
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions.
    Bhattacharyya M; Vishveshwara S
    Mol Biosyst; 2011 Jul; 7(7):2320-30. PubMed ID: 21617814
    [TBL] [Abstract][Full Text] [Related]  

  • 7. ENCORE: Software for Quantitative Ensemble Comparison.
    Tiberti M; Papaleo E; Bengtsen T; Boomsma W; Lindorff-Larsen K
    PLoS Comput Biol; 2015 Oct; 11(10):e1004415. PubMed ID: 26505632
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Clustering molecular dynamics trajectories for optimizing docking experiments.
    De Paris R; Quevedo CV; Ruiz DD; Norberto de Souza O; Barros RC
    Comput Intell Neurosci; 2015; 2015():916240. PubMed ID: 25873944
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Boosted neural networks scoring functions for accurate ligand docking and ranking.
    Ashtawy HM; Mahapatra NR
    J Bioinform Comput Biol; 2018 Apr; 16(2):1850004. PubMed ID: 29495922
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Ensemble-based docking using biased molecular dynamics.
    Campbell AJ; Lamb ML; Joseph-McCarthy D
    J Chem Inf Model; 2014 Jul; 54(7):2127-38. PubMed ID: 24881672
    [TBL] [Abstract][Full Text] [Related]  

  • 11. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.
    Estrada T; Zhang B; Cicotti P; Armen RS; Taufer M
    Comput Biol Med; 2012 Jul; 42(7):758-71. PubMed ID: 22658682
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches.
    Motta S; Bonati L
    J Chem Inf Model; 2017 Jul; 57(7):1563-1578. PubMed ID: 28616990
    [TBL] [Abstract][Full Text] [Related]  

  • 13. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.
    Conev A; Rigo MM; Devaurs D; Fonseca AF; Kalavadwala H; de Freitas MV; Clementi C; Zanatta G; Antunes DA; Kavraki LE
    Brief Bioinform; 2023 Jul; 24(4):. PubMed ID: 37418278
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations.
    Uehara S; Tanaka S
    J Chem Inf Model; 2017 Apr; 57(4):742-756. PubMed ID: 28388074
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone.
    Stetz G; Tse A; Verkhivker GM
    PLoS One; 2017; 12(11):e0186089. PubMed ID: 29095844
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking.
    Strecker C; Meyer B
    J Chem Inf Model; 2018 May; 58(5):1121-1131. PubMed ID: 29683661
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Simple, yet powerful methodologies for conformational sampling of proteins.
    Harada R; Takano Y; Baba T; Shigeta Y
    Phys Chem Chem Phys; 2015 Mar; 17(9):6155-73. PubMed ID: 25659594
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Improving the performance of self-organizing maps via growing representations.
    Merkow M; DeLisle RK
    J Chem Inf Model; 2007; 47(5):1797-807. PubMed ID: 17705465
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Eurecon: Equidistant uniform rigid-body ensemble constructor.
    Popov P; Grudinin S
    J Mol Graph Model; 2018 Mar; 80():313-319. PubMed ID: 29427936
    [TBL] [Abstract][Full Text] [Related]  

  • 20. MIANN models in medicinal, physical and organic chemistry.
    González-Díaz H; Arrasate S; Sotomayor N; Lete E; Munteanu CR; Pazos A; Besada-Porto L; Ruso JM
    Curr Top Med Chem; 2013; 13(5):619-41. PubMed ID: 23548024
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.