229 related articles for article (PubMed ID: 33939083)
1. A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge.
Ghorbani M; Hudson PS; Jones MR; Aviat F; Meana-Pañeda R; Klauda JB; Brooks BR
J Comput Aided Mol Des; 2021 May; 35(5):667-677. PubMed ID: 33939083
[TBL] [Abstract][Full Text] [Related]
2. Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange.
Markthaler D; Kraus H; Hansen N
J Comput Aided Mol Des; 2022 Jan; 36(1):1-9. PubMed ID: 34978001
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method.
Han K; Hudson PS; Jones MR; Nishikawa N; Tofoleanu F; Brooks BR
J Comput Aided Mol Des; 2018 Oct; 32(10):1059-1073. PubMed ID: 30084077
[TBL] [Abstract][Full Text] [Related]
5. Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field.
Laury ML; Wang Z; Gordon AS; Ponder JW
J Comput Aided Mol Des; 2018 Oct; 32(10):1087-1095. PubMed ID: 30324303
[TBL] [Abstract][Full Text] [Related]
6. Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.
Song LF; Bansal N; Zheng Z; Merz KM
J Comput Aided Mol Des; 2018 Oct; 32(10):1013-1026. PubMed ID: 30143917
[TBL] [Abstract][Full Text] [Related]
7. Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.
Hudson PS; Aviat F; Meana-Pañeda R; Warrensford L; Pollard BC; Prasad S; Jones MR; Woodcock HL; Brooks BR
J Comput Aided Mol Des; 2022 Apr; 36(4):263-277. PubMed ID: 35597880
[TBL] [Abstract][Full Text] [Related]
8. Thermodynamic integration to predict host-guest binding affinities.
Lawrenz M; Wereszczynski J; Ortiz-Sánchez JM; Nichols SE; McCammon JA
J Comput Aided Mol Des; 2012 May; 26(5):569-76. PubMed ID: 22350568
[TBL] [Abstract][Full Text] [Related]
9. SAMPL6 host-guest challenge: binding free energies via a multistep approach.
Eken Y; Patel P; Díaz T; Jones MR; Wilson AK
J Comput Aided Mol Des; 2018 Oct; 32(10):1097-1115. PubMed ID: 30225724
[TBL] [Abstract][Full Text] [Related]
10. Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.
Monroe JI; Shirts MR
J Comput Aided Mol Des; 2014 Apr; 28(4):401-15. PubMed ID: 24610238
[TBL] [Abstract][Full Text] [Related]
11. Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics.
Hsiao YW; Söderhjelm P
J Comput Aided Mol Des; 2014 Apr; 28(4):443-54. PubMed ID: 24535628
[TBL] [Abstract][Full Text] [Related]
12. The SAMPL4 host-guest blind prediction challenge: an overview.
Muddana HS; Fenley AT; Mobley DL; Gilson MK
J Comput Aided Mol Des; 2014 Apr; 28(4):305-17. PubMed ID: 24599514
[TBL] [Abstract][Full Text] [Related]
13. Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.
Dixon T; Lotz SD; Dickson A
J Comput Aided Mol Des; 2018 Oct; 32(10):1001-1012. PubMed ID: 30141102
[TBL] [Abstract][Full Text] [Related]
14. AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.
Shi Y; Laury ML; Wang Z; Ponder JW
J Comput Aided Mol Des; 2021 Jan; 35(1):79-93. PubMed ID: 33140208
[TBL] [Abstract][Full Text] [Related]
15. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction.
Velez-Vega C; Gilson MK
J Comput Chem; 2013 Oct; 34(27):2360-71. PubMed ID: 24038118
[TBL] [Abstract][Full Text] [Related]
16. Overview of the SAMPL6 host-guest binding affinity prediction challenge.
Rizzi A; Murkli S; McNeill JN; Yao W; Sullivan M; Gilson MK; Chiu MW; Isaacs L; Gibb BC; Mobley DL; Chodera JD
J Comput Aided Mol Des; 2018 Oct; 32(10):937-963. PubMed ID: 30415285
[TBL] [Abstract][Full Text] [Related]
17. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.
Lee J; Miller BT; Brooks BR
Protein Sci; 2016 Jan; 25(1):231-43. PubMed ID: 26189656
[TBL] [Abstract][Full Text] [Related]
18. An overview of the SAMPL8 host-guest binding challenge.
Amezcua M; Setiadi J; Ge Y; Mobley DL
J Comput Aided Mol Des; 2022 Oct; 36(10):707-734. PubMed ID: 36229622
[TBL] [Abstract][Full Text] [Related]
19. Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling.
Boz E; Stein M
Int J Mol Sci; 2021 Mar; 22(6):. PubMed ID: 33802920
[TBL] [Abstract][Full Text] [Related]
20. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.
Henriksen NM; Fenley AT; Gilson MK
J Chem Theory Comput; 2015 Sep; 11(9):4377-94. PubMed ID: 26523125
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]