These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

133 related articles for article (PubMed ID: 27248478)

  • 21. Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water.
    Woods CJ; Malaisree M; Michel J; Long B; McIntosh-Smith S; Mulholland AJ
    Faraday Discuss; 2014; 169():477-99. PubMed ID: 25340314
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Energetic contributions of amino acid residues and its cross-talk to delineate ligand-binding mechanism.
    Kumar SP; Patel CN; Rawal RM; Pandya HA
    Proteins; 2020 Sep; 88(9):1207-1225. PubMed ID: 32323374
    [TBL] [Abstract][Full Text] [Related]  

  • 23. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
    Kaus JW; Harder E; Lin T; Abel R; McCammon JA; Wang L
    J Chem Theory Comput; 2015 Jun; 11(6):2670-9. PubMed ID: 26085821
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.
    Zhang S; Hahn DF; Shirts MR; Voelz VA
    J Chem Theory Comput; 2021 Oct; 17(10):6536-6547. PubMed ID: 34516130
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation.
    Rifai EA; Ferrario V; Pleiss J; Geerke DP
    J Chem Theory Comput; 2020 Feb; 16(2):1300-1310. PubMed ID: 31894691
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Predicting absolute ligand binding free energies to a simple model site.
    Mobley DL; Graves AP; Chodera JD; McReynolds AC; Shoichet BK; Dill KA
    J Mol Biol; 2007 Aug; 371(4):1118-34. PubMed ID: 17599350
    [TBL] [Abstract][Full Text] [Related]  

  • 27. A QM protein-ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R).
    Ekhteiari Salmas R; Serhat Is Y; Durdagi S; Stein M; Yurtsever M
    J Biomol Struct Dyn; 2018 Aug; 36(10):2668-2677. PubMed ID: 28805144
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?
    Mulakala C; Viswanadhan VN
    J Mol Graph Model; 2013 Nov; 46():41-51. PubMed ID: 24121518
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Thermodynamic investigation of hirudin binding to the slow and fast forms of thrombin: evidence for folding transitions in the inhibitor and protease coupled to binding.
    Ayala YM; Vindigni A; Nayal M; Spolar RS; Record MT; Di Cera E
    J Mol Biol; 1995 Nov; 253(5):787-98. PubMed ID: 7473752
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Profiling the structural determinants for the selectivity of representative factor-Xa and thrombin inhibitors using combined ligand-based and structure-based approaches.
    Bhunia SS; Roy KK; Saxena AK
    J Chem Inf Model; 2011 Aug; 51(8):1966-85. PubMed ID: 21761917
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding.
    Boulton S; Van K; VanSchouwen B; Augustine J; Akimoto M; Melacini G
    Biophys J; 2020 Sep; 119(6):1135-1146. PubMed ID: 32882185
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Electrostatic steering and ionic tethering in the formation of thrombin-hirudin complexes: the role of the thrombin anion-binding exosite-I.
    Myles T; Le Bonniec BF; Betz A; Stone SR
    Biochemistry; 2001 Apr; 40(16):4972-9. PubMed ID: 11305913
    [TBL] [Abstract][Full Text] [Related]  

  • 33. Rescoring of docking poses under Occam's Razor: are there simpler solutions?
    Zhenin M; Bahia MS; Marcou G; Varnek A; Senderowitz H; Horvath D
    J Comput Aided Mol Des; 2018 Sep; 32(9):877-888. PubMed ID: 30173397
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
    Deng N; Flynn WF; Xia J; Vijayan RS; Zhang B; He P; Mentes A; Gallicchio E; Levy RM
    J Comput Aided Mol Des; 2016 Sep; 30(9):743-751. PubMed ID: 27562018
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water.
    Cozzini P; Fornabaio M; Marabotti A; Abraham DJ; Kellogg GE; Mozzarelli A
    J Med Chem; 2002 Jun; 45(12):2469-83. PubMed ID: 12036355
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.
    Minh DDL
    J Comput Chem; 2020 Mar; 41(7):715-730. PubMed ID: 31397498
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies.
    Liu X; Peng L; Zhou Y; Zhang Y; Zhang JZH
    J Chem Theory Comput; 2018 Mar; 14(3):1772-1780. PubMed ID: 29406753
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.
    Duan LL; Feng GQ; Zhang QG
    Sci Rep; 2016 Aug; 6():31488. PubMed ID: 27507430
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide.
    Aldeghi M; Bluck JP; Biggin PC
    Methods Mol Biol; 2018; 1762():199-232. PubMed ID: 29594774
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin.
    Biela A; Khayat M; Tan H; Kong J; Heine A; Hangauer D; Klebe G
    J Mol Biol; 2012 May; 418(5):350-66. PubMed ID: 22366545
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 7.