202 related articles for article (PubMed ID: 30324304)
1. Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.
Nishikawa N; Han K; Wu X; Tofoleanu F; Brooks BR
J Comput Aided Mol Des; 2018 Oct; 32(10):1075-1086. PubMed ID: 30324304
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.
Tofoleanu F; Lee J; Pickard Iv FC; König G; Huang J; Baek M; Seok C; Brooks BR
J Comput Aided Mol Des; 2017 Jan; 31(1):107-118. PubMed ID: 27696242
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. 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]
6. Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.
Caldararu O; Olsson MA; Misini Ignjatović M; Wang M; Ryde U
J Comput Aided Mol Des; 2018 Oct; 32(10):1027-1046. PubMed ID: 30203229
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. 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]
9. Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.
Papadourakis M; Bosisio S; Michel J
J Comput Aided Mol Des; 2018 Oct; 32(10):1047-1058. PubMed ID: 30159717
[TBL] [Abstract][Full Text] [Related]
10. SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.
Sun Z; He Q; Li X; Zhu Z
J Comput Aided Mol Des; 2020 May; 34(5):589-600. PubMed ID: 31974852
[TBL] [Abstract][Full Text] [Related]
11. SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach.
Procacci P; Guarrasi M; Guarnieri G
J Comput Aided Mol Des; 2018 Oct; 32(10):965-982. PubMed ID: 30128927
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. 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]
14. SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics.
Eken Y; Almeida NMS; Wang C; Wilson AK
J Comput Aided Mol Des; 2021 Jan; 35(1):63-77. PubMed ID: 33150463
[TBL] [Abstract][Full Text] [Related]
15. Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges.
Casbarra L; Procacci P
J Comput Aided Mol Des; 2021 Jun; 35(6):721-729. PubMed ID: 34027592
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.
Bansal N; Zheng Z; Cerutti DS; Merz KM
J Comput Aided Mol Des; 2017 Jan; 31(1):47-60. PubMed ID: 27699553
[TBL] [Abstract][Full Text] [Related]
18. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
Yin J; Henriksen NM; Slochower DR; Gilson MK
J Comput Aided Mol Des; 2017 Jan; 31(1):133-145. PubMed ID: 27638809
[TBL] [Abstract][Full Text] [Related]
19. Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.
Mikulskis P; Cioloboc D; Andrejić M; Khare S; Brorsson J; Genheden S; Mata RA; Söderhjelm P; Ryde U
J Comput Aided Mol Des; 2014 Apr; 28(4):375-400. PubMed ID: 24700414
[TBL] [Abstract][Full Text] [Related]
20. Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.
Hudson PS; Han K; Woodcock HL; Brooks BR
J Comput Aided Mol Des; 2018 Oct; 32(10):983-999. PubMed ID: 30276502
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
