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drugdata/D3R: Evaluation Improvements

Authors: Chris Churas; shuail; j-wags; rvswift; nadyawilliams;

drugdata/D3R: Evaluation Improvements

Abstract

EvaluationTask modified to pass path to blastnfilter task to evaluate.py. Issue #139 Median RMSD added to post_evaluation.py outputs. Issue #136 Added histogram of RMSD scores to post_evaluation.py outputs. Issue #137 Continuously output the analysis result into the pickle csv and txt files. Issue #133 Align the docked complex using the binding site alignment for each of the crystal template and calculate the RMSD, if the binding site alignment failed, then the whole protein alignment will be applied Improve the extraction step in the evaluate.py to ensure the RMSD calculating was only applied to the docked ligand but not all others ligand like solvents or co-factors Add the ligand center calculation step in the evaluate.py to output the distance of the docked ligand with the crystal ligand. Also calculate the distance between the original LMCSS ligand center with the crystal ligand center Update the genchallengedata.py to extract Apo chain which is closed to the LMCSS ligand. Issue #135

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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