167 related articles for article (PubMed ID: 31397498)
1. 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]
2. Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors.
Xie B; Minh DDL
J Comput Aided Mol Des; 2019 Jan; 33(1):61-69. PubMed ID: 30084078
[TBL] [Abstract][Full Text] [Related]
3. Using the fast fourier transform in binding free energy calculations.
Nguyen TH; Zhou HX; Minh DDL
J Comput Chem; 2018 Apr; 39(11):621-636. PubMed ID: 29270990
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Power transformations improve interpolation of grids for molecular mechanics interaction energies.
Minh DDL
J Comput Chem; 2018 Jul; 39(19):1200-1207. PubMed ID: 29457253
[TBL] [Abstract][Full Text] [Related]
6. Implicit ligand theory for relative binding free energies.
Nguyen TH; Minh DDL
J Chem Phys; 2018 Mar; 148(10):104114. PubMed ID: 29544299
[TBL] [Abstract][Full Text] [Related]
7. Advances in Docking.
Sulimov VB; Kutov DC; Sulimov AV
Curr Med Chem; 2019; 26(42):7555-7580. PubMed ID: 30182836
[TBL] [Abstract][Full Text] [Related]
8. Protein-Ligand Binding Free Energy Calculations with FEP.
Wang L; Chambers J; Abel R
Methods Mol Biol; 2019; 2022():201-232. PubMed ID: 31396905
[TBL] [Abstract][Full Text] [Related]
9. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.
Minh DD
J Chem Phys; 2012 Sep; 137(10):104106. PubMed ID: 22979849
[TBL] [Abstract][Full Text] [Related]
10. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
Rizzi A; Jensen T; Slochower DR; Aldeghi M; Gapsys V; Ntekoumes D; Bosisio S; Papadourakis M; Henriksen NM; de Groot BL; Cournia Z; Dickson A; Michel J; Gilson MK; Shirts MR; Mobley DL; Chodera JD
J Comput Aided Mol Des; 2020 May; 34(5):601-633. PubMed ID: 31984465
[TBL] [Abstract][Full Text] [Related]
11. SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.
Huai Z; Yang H; Li X; Sun Z
J Comput Aided Mol Des; 2021 Jan; 35(1):117-129. PubMed ID: 33037549
[TBL] [Abstract][Full Text] [Related]
12. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.
Jiang W; Thirman J; Jo S; Roux B
J Phys Chem B; 2018 Oct; 122(41):9435-9442. PubMed ID: 30253098
[TBL] [Abstract][Full Text] [Related]
13. Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.
Sakae Y; Zhang BW; Levy RM; Deng N
J Comput Chem; 2020 Jan; 41(1):56-68. PubMed ID: 31621932
[TBL] [Abstract][Full Text] [Related]
14. Free energy calculations of protein-ligand interactions.
de Ruiter A; Oostenbrink C
Curr Opin Chem Biol; 2011 Aug; 15(4):547-52. PubMed ID: 21684797
[TBL] [Abstract][Full Text] [Related]
15. Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols.
Bhati AP; Coveney PV
J Chem Theory Comput; 2022 Apr; 18(4):2687-2702. PubMed ID: 35293737
[TBL] [Abstract][Full Text] [Related]
16. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
Lee J; Tofoleanu F; Pickard FC; König G; Huang J; Damjanović A; Baek M; Seok C; Brooks BR
J Comput Aided Mol Des; 2017 Jan; 31(1):71-85. PubMed ID: 27677749
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. 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]
19. Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.
Alcantara J; Chiu K; Bickel JD; Rizzo RC; Simmerling C
J Chem Theory Comput; 2023 Nov; 19(21):7934-7945. PubMed ID: 37831619
[TBL] [Abstract][Full Text] [Related]
20. PSI-DOCK: towards highly efficient and accurate flexible ligand docking.
Pei J; Wang Q; Liu Z; Li Q; Yang K; Lai L
Proteins; 2006 Mar; 62(4):934-46. PubMed ID: 16395666
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
