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.
125 related articles for article (PubMed ID: 34625885)
21. Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Khalak Y; Tresadern G; de Groot BL; Gapsys V J Comput Aided Mol Des; 2021 Jan; 35(1):49-61. PubMed ID: 33230742 [TBL] [Abstract][Full Text] [Related]
22. Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality. Echeverria I; Amzel LM J Phys Chem B; 2012 Sep; 116(36):10986-95. PubMed ID: 22849340 [TBL] [Abstract][Full Text] [Related]
23. Combining Monte Carlo and Molecular Dynamics Simulations for Enhanced Binding Free Energy Estimation through Markov State Models. Gilabert JF; Gracia Carmona O; Hogner A; Guallar V J Chem Inf Model; 2020 Nov; 60(11):5529-5539. PubMed ID: 32644807 [TBL] [Abstract][Full Text] [Related]
24. Alchemical prediction of hydration free energies for SAMPL. Mobley DL; Liu S; Cerutti DS; Swope WC; Rice JE J Comput Aided Mol Des; 2012 May; 26(5):551-62. PubMed ID: 22198475 [TBL] [Abstract][Full Text] [Related]
25. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations. Baumann HM; Gapsys V; de Groot BL; Mobley DL J Phys Chem B; 2021 May; 125(17):4241-4261. PubMed ID: 33905257 [TBL] [Abstract][Full Text] [Related]
26. Exploring the Effect of Enhanced Sampling on Protein Stability Prediction. Markthaler D; Fleck M; Stankiewicz B; Hansen N J Chem Theory Comput; 2022 Apr; 18(4):2569-2583. PubMed ID: 35298174 [TBL] [Abstract][Full Text] [Related]
27. 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]
28. 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]
29. Partition coefficients for the SAMPL5 challenge using transfer free energies. Jones MR; Brooks BR; Wilson AK J Comput Aided Mol Des; 2016 Nov; 30(11):1129-1138. PubMed ID: 27646287 [TBL] [Abstract][Full Text] [Related]
30. DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression. Liu T; Simine L J Chem Inf Model; 2024 Jul; 64(14):5617-5623. PubMed ID: 38980667 [TBL] [Abstract][Full Text] [Related]
31. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. Arcon JP; Defelipe LA; Modenutti CP; López ED; Alvarez-Garcia D; Barril X; Turjanski AG; Martí MA J Chem Inf Model; 2017 Apr; 57(4):846-863. PubMed ID: 28318252 [TBL] [Abstract][Full Text] [Related]
32. 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]
33. 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]
34. Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions. Wan S; Bhati AP; Coveney PV J Chem Theory Comput; 2023 Nov; 19(21):7846-7860. PubMed ID: 37862058 [TBL] [Abstract][Full Text] [Related]
35. Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. Wang S; Riniker S J Comput Aided Mol Des; 2020 Apr; 34(4):393-403. PubMed ID: 31745704 [TBL] [Abstract][Full Text] [Related]
36. Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach. Procacci P J Chem Theory Comput; 2022 Jun; 18(6):4014-4026. PubMed ID: 35642423 [TBL] [Abstract][Full Text] [Related]
37. On the estimation of the free energy, from a single equilibrium statistical ensemble, via particle reinsertion. Boulougouris GC J Phys Chem B; 2012 Jan; 116(3):997-1006. PubMed ID: 22168469 [TBL] [Abstract][Full Text] [Related]
38. Stacking Gaussian processes to improve [Formula: see text] predictions in the SAMPL7 challenge. Raddi RM; Voelz VA J Comput Aided Mol Des; 2021 Sep; 35(9):953-961. PubMed ID: 34363562 [TBL] [Abstract][Full Text] [Related]
39. Taming Rugged Free Energy Landscapes Using an Average Force. Fu H; Shao X; Cai W; Chipot C Acc Chem Res; 2019 Nov; 52(11):3254-3264. PubMed ID: 31680510 [TBL] [Abstract][Full Text] [Related]
40. Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories. Morishita T; Yonezawa Y; Ito AM J Chem Theory Comput; 2017 Jul; 13(7):3106-3119. PubMed ID: 28602083 [TBL] [Abstract][Full Text] [Related] [Previous] [Next] [New Search]