rando2
commented
2 years ago Thank you @agitter! I got super bogged down in the ivermectin literature today, but plan to address this topic tomorrow!
Open agitter opened 2 years ago
rando2
commented
2 years ago Thank you @agitter! I got super bogged down in the ivermectin literature today, but plan to address this topic tomorrow!
Title: A critical overview of computational approaches employed for COVID-19 drug discovery
Please paste a link to the paper or a citation here:
Link: https://doi.org/10.1039/D0CS01065K
What is the paper's Manubot-style citation?
Citation: doi:10.1039/D0CS01065K
Please list some keywords (3-10) that help identify the relevance of this paper to COVID-19
Please note the publication / review status
Which areas of expertise are particularly relevant to the paper?
Questions to answer about each paper:
Please provide 1-2 sentences introducing the study and its main findings
@rando2 this review on computational methods that have been applied for drug discovery and repurposing may help answer questions we had about how much repurposing has contributed versus experimental screening and other strategies.
Study question(s) being investigated:
How many/what drugs/combinations are being considered?
What are the main hypotheses being tested?
Study population:
What is the model system (e.g., human study, animal model, cell line study)?
What is the sample size? If multiple groups are considered, give sample size for each group (including controls).
For human studies:
What countries/regions are considered?
What is the age range, gender, other relevant characteristics?
What is the setting of the study (random sample of school children, inpatient, outpatient, etc)?
What other specific inclusion-exclusion criteria are considered?
For example, do the investigators exclude patients with diagnosed neoplasms or patients over/under a certain age?
Treatment assignment:
How are treatments assigned?
For example, is it an interventional or an observational study?
Is the study randomized?
A study can be interventional but not randomized (e.g., a phase I or II clinical trial is interventional but often not randomized).
Provide other relevant details about the design.
This includes possible treatment stratification (e.g., within litters for animal studies, within hospitals for human studies), possible confounding variables (e.g., having a large age range of individuals), possible risks of bias and how they are addressed (e.g., is there masking in a clinical trial? how are individuals chosen in an observational study?).
Outcome Assessment:
Describe the outcome that is assessed and whether it is appropriate.
For example: Is the outcome assessed by a clinician or is it self-reported? Is the outcome based on viral load or a functional measurement (e.g., respiratory function, discharge from hospital)? What method is used to measure the outcome? How long after a treatment is the outcome measured?
Are outcome measurements complete?
For example, are there individuals lost to follow up?
Are outcome measurements subject to various kinds of bias?
For example, a lack of masking in randomized clinical trials.
Statistical Methods Assessment:
What methods are used for inference?
For example, logistic regression, nonparametric methods.
Are the methods appropriate for the study?
For example, are clustered data treated independently or are clusters adjusted for, such as different hospitals or litters?
Are adjustments made for possible confounders?
For example, adjustment for age, sex, or comorbidities.
Results Summary:
What is the estimated association?
For example, is it an estimated odds ratio, a median difference in detected cases, etc?
What measures of confidence or statistical significance are provided?
For example, confidence intervals, p-values, and/or Bayes factors.
Interpretation of results for study population:
Can we make a causal interpretation for the individuals in the study of drug -> outcome, such as "taking drug A improves likelihood of survival twofold over taking drug B."
For example, with a well-performed animal study or randomized trial it is often possible to infer causality. If is an observational study, does it match up with some of the Bradford Hill criteria? https://www.edwardtufte.com/tufte/hill https://en.wikipedia.org/wiki/Bradford_Hill_criteria
Are there identified side effects or interactions with other drugs?
For example, is the treatment known to cause liver damage or to not be prescribed for individuals with certain comorbities?
Are there specific subgroups with different findings?
For example, do individuals with a specific baseline seem to do particularly well? Be particularly cautious with respect to multiple testing here.
Extrapolation of conclusions to other groups of individuals not specifically included in the study:
If the study is an animal study, which animal and how relevant is that model?
Is the model system appropriate? Is there evidence from past use that it's highly-relevant to therapeutic design in this context?
If it is a human study, what characteristics of the study population may support/limit extrapolation?
Summary of reliability
1-2 sentences on concluding remarks, including summary of strengths, weaknesses, limitations.
Progress
Check off the components as they are completed. If the component is not applicable, check the box as well.