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.
2. SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges. Riquelme M; Vöhringer-Martinez E J Comput Aided Mol Des; 2020 Apr; 34(4):327-334. PubMed ID: 31960251 [TBL] [Abstract][Full Text] [Related]
3. Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host-Guest Affinity Predictions. González D; Macaya L; Castillo-Orellana C; Verstraelen T; Vogt-Geisse S; Vöhringer-Martinez E J Chem Inf Model; 2022 Sep; 62(17):4162-4174. PubMed ID: 35959540 [TBL] [Abstract][Full Text] [Related]
4. Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges. Lara A; Riquelme M; Vöhringer-Martinez E J Comput Chem; 2018 Aug; 39(22):1728-1737. PubMed ID: 29752734 [TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. 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]
8. Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant. Macaya L; González D; Vöhringer-Martinez E J Chem Inf Model; 2024 Apr; 64(8):3269-3277. PubMed ID: 38546407 [TBL] [Abstract][Full Text] [Related]
9. 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]
10. A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges. Kelly BD; Smith WR ACS Omega; 2020 Jul; 5(28):17170-17181. PubMed ID: 32715202 [TBL] [Abstract][Full Text] [Related]
11. SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. Amezcua M; El Khoury L; Mobley DL J Comput Aided Mol Des; 2021 Jan; 35(1):1-35. PubMed ID: 33392951 [TBL] [Abstract][Full Text] [Related]
12. Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge. Bosisio S; Mey ASJS; Michel J J Comput Aided Mol Des; 2017 Jan; 31(1):61-70. PubMed ID: 27503495 [TBL] [Abstract][Full Text] [Related]
13. Overview of the SAMPL5 host-guest challenge: Are we doing better? Yin J; Henriksen NM; Slochower DR; Shirts MR; Chiu MW; Mobley DL; Gilson MK J Comput Aided Mol Des; 2017 Jan; 31(1):1-19. PubMed ID: 27658802 [TBL] [Abstract][Full Text] [Related]
15. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). Caldararu O; Olsson MA; Riplinger C; Neese F; Ryde U J Comput Aided Mol Des; 2017 Jan; 31(1):87-106. PubMed ID: 27600554 [TBL] [Abstract][Full Text] [Related]
16. Alchemical Hydration Free-Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On-the-Fly Polarization Approach. Kelly BD; Smith WR J Chem Theory Comput; 2020 Feb; 16(2):1146-1161. PubMed ID: 31930918 [TBL] [Abstract][Full Text] [Related]
17. Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. Riquelme M; Lara A; Mobley DL; Verstraelen T; Matamala AR; Vöhringer-Martinez E J Chem Inf Model; 2018 Sep; 58(9):1779-1797. PubMed ID: 30125107 [TBL] [Abstract][Full Text] [Related]
18. 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]
19. Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [M Norjmaa G; Vidossich P; Maréchal JD; Ujaque G J Chem Inf Model; 2021 Sep; 61(9):4370-4381. PubMed ID: 34505774 [TBL] [Abstract][Full Text] [Related]
20. 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] [Next] [New Search]