2023
DOI: 10.1021/acs.jctc.3c00109
|View full text |Cite
|
Sign up to set email alerts
|

Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules

Abstract: Determining the presence of water molecules at protein–ligand interfaces is still a challenging task in free-energy calculations. The inappropriate placement of water molecules results in the stabilization of wrong conformational orientations of the ligand. With classical alchemical perturbation methods, such as thermodynamic integration (TI), it is essential to know the amount of water molecules in the active site of the respective ligands. However, the resolution of the crystal structure and the correct assi… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2

Citation Types

0
2
0

Year Published

2024
2024
2024
2024

Publication Types

Select...
1

Relationship

0
1

Authors

Journals

citations
Cited by 1 publication
(2 citation statements)
references
References 58 publications
0
2
0
Order By: Relevance
“…Performing multiple-independent simulation repeats allows for more reliable phase space exploration and uncertainty estimation. , Sampling improvements in relative free energy calculations may also arise by optimally planning the perturbations to be calculated, altering the alchemical pathway, using different atom mapping as in the separated topology approach, or using no atom mapping at all as in enveloping distribution sampling. To sample the water position sufficiently, enhanced water sampling protocols , can be employed. Multiple options exist, such as explicit water perturbations, Monte Carlo moves, ,, or grand canonical ensemble simulations. …”
Section: Introductionmentioning
confidence: 99%
See 1 more Smart Citation
“…Performing multiple-independent simulation repeats allows for more reliable phase space exploration and uncertainty estimation. , Sampling improvements in relative free energy calculations may also arise by optimally planning the perturbations to be calculated, altering the alchemical pathway, using different atom mapping as in the separated topology approach, or using no atom mapping at all as in enveloping distribution sampling. To sample the water position sufficiently, enhanced water sampling protocols , can be employed. Multiple options exist, such as explicit water perturbations, Monte Carlo moves, ,, or grand canonical ensemble simulations. …”
Section: Introductionmentioning
confidence: 99%
“… 34 37 To sample the water position sufficiently, enhanced water sampling protocols 38 , 39 can be employed. Multiple options exist, such as explicit water perturbations, 40 Monte Carlo moves, 23 , 41 , 42 or grand canonical ensemble simulations. 43 45 …”
Section: Introductionmentioning
confidence: 99%