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Efficient iterative virtual screening with Apache Spark and conformal prediction

Overview of attention for article published in Journal of Cheminformatics, March 2018
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (83rd percentile)

Mentioned by

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22 tweeters

Citations

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4 Dimensions

Readers on

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27 Mendeley
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Title
Efficient iterative virtual screening with Apache Spark and conformal prediction
Published in
Journal of Cheminformatics, March 2018
DOI 10.1186/s13321-018-0265-z
Pubmed ID
Authors

Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Toor, Wesley Schaal, Erwin Laure, Ola Spjuth

Abstract

Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out on computer clusters or on large workstations in a brute force manner, by docking and scoring all available ligands. In this study we propose a strategy that is based on iteratively docking a set of ligands to form a training set, training a ligand-based model on this set, and predicting the remainder of the ligands to exclude those predicted as 'low-scoring' ligands. Then, another set of ligands are docked, the model is retrained and the process is repeated until a certain model efficiency level is reached. Thereafter, the remaining ligands are docked or excluded based on this model. We use SVM and conformal prediction to deliver valid prediction intervals for ranking the predicted ligands, and Apache Spark to parallelize both the docking and the modeling. We show on 4 different targets that conformal prediction based virtual screening (CPVS) is able to reduce the number of docked molecules by 62.61% while retaining an accuracy for the top 30 hits of 94% on average and a speedup of 3.7. The implementation is available as open source via GitHub ( https://github.com/laeeq80/spark-cpvs ) and can be run on high-performance computers as well as on cloud resources.

Twitter Demographics

The data shown below were collected from the profiles of 22 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 27 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 27 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 33%
Student > Master 4 15%
Student > Bachelor 4 15%
Professor > Associate Professor 3 11%
Researcher 3 11%
Other 4 15%
Readers by discipline Count As %
Computer Science 10 37%
Chemistry 9 33%
Engineering 3 11%
Agricultural and Biological Sciences 2 7%
Decision Sciences 1 4%
Other 2 7%

Attention Score in Context

This research output has an Altmetric Attention Score of 12. 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 20 September 2018.
All research outputs
#1,397,364
of 13,999,320 outputs
Outputs from Journal of Cheminformatics
#153
of 566 outputs
Outputs of similar age
#45,713
of 274,458 outputs
Outputs of similar age from Journal of Cheminformatics
#1
of 1 outputs
Altmetric has tracked 13,999,320 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 566 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 9.2. This one has gotten more attention than average, scoring higher than 72% of its peers.
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 274,458 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 83% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them