| Title |
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
|
|---|---|
| Published in |
Perspectives in Drug Discovery and Design, July 2016
|
| DOI | 10.1007/s10822-016-9926-z |
| Pubmed ID | |
| Authors |
Samuel Genheden, Jonathan W. Essex |
| Abstract |
We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 21 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Czechia | 1 | 5% |
| Unknown | 20 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 9 | 43% |
| Student > Ph. D. Student | 5 | 24% |
| Professor | 2 | 10% |
| Student > Master | 1 | 5% |
| Unknown | 4 | 19% |
| Readers by discipline | Count | As % |
|---|---|---|
| Chemistry | 9 | 43% |
| Chemical Engineering | 2 | 10% |
| Biochemistry, Genetics and Molecular Biology | 2 | 10% |
| Mathematics | 1 | 5% |
| Computer Science | 1 | 5% |
| Other | 1 | 5% |
| Unknown | 5 | 24% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 August 2016.
All research outputs
#19,985,400
of 25,457,297 outputs
Outputs from Perspectives in Drug Discovery and Design
#806
of 949 outputs
Outputs of similar age
#282,782
of 380,243 outputs
Outputs of similar age from Perspectives in Drug Discovery and Design
#21
of 25 outputs
Altmetric has tracked 25,457,297 research outputs across all sources so far. This one is in the 21st percentile – i.e., 21% of other outputs scored the same or lower than it.
So far Altmetric has tracked 949 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.3. This one is in the 15th percentile – i.e., 15% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 380,243 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 25th percentile – i.e., 25% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 25 others from the same source and published within six weeks on either side of this one. This one is in the 16th percentile – i.e., 16% of its contemporaries scored the same or lower than it.