ReviewJournal of cheminformatics2020
Towards reproducible computational drug discovery.
Review in Journal of cheminformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
72 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Interoperability of heterogeneous health information systems: a systematic literature review.BMC medical informatics and decision making · 2023Pooled it
- From Chemical Scaffold to Predicted Toxicity: A Scaffold-Aware Pipeline for Reliable In Silico Prioritization ofInternational journal of molecular sciences · 2026Article
- In silico discovery of CETP inhibitors from ZINC15 compounds using docking, ADMET filtering, and molecular dynamics simulations.Research in pharmaceutical sciences · 2026Article
- Critical Artifacts Improve Reproducibility of Protein-Ligand Binding Affinity Prediction Models on CASF-2016.Journal of chemical information and modeling · 2026Article
- Transformer-accelerated discovery of inhibitors targeting the RpsAJournal of cheminformatics · 2026Article
- Analyzing the Chemical Space of Opioid Receptor Agonists and Antagonists: Insights from Computational Models.ACS omega · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Data curation in cheminformatics: importance and implementation.Journal of cheminformatics · 2026Review
- AI accelerate the identification of druggable targets by 3D structures of proteins and compounds.NPJ precision oncology · 2026Review
- Big Data for Drug Discovery: Some Historical Landscape, Considerations, and Applications for a Medicinal Chemist.ACS omega · 2026Review
- Machine Learning Application in Enhancing HIV Management and Treatment Outcomes: Revolutionizing HIV Infection.Current HIV research · 2026Review
- A Systematic Review of Drug-Related InteractionsUtilizing Deep Learning and LLMs for Prediction and Mitigation.ACS omega · 2025Review
- Computational Chemistry Advances in the Development of PARP1 Inhibitors for Breast Cancer Therapy.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Combinatorial QM and MD in silico design of natural product-based DHFR inhibitors.Scientific reports · 2025Article
- Advancing ADMET prediction through multiscale fragment-aware pretraining with MSformer-ADMET.Briefings in bioinformatics · 2025Article
- Improving drug-induced liver injury prediction using graph neural networks with augmented graph features from molecular optimisation.Journal of cheminformatics · 2025Article
- OnSIDES database: Extracting adverse drug events from drug labels using natural language processing models.Med (New York, N.Y.) · 2025Article
- Perturbation-Theory Machine Learning for Multi-Target Drug Discovery in Modern Anticancer Research.Current issues in molecular biology · 2025Review
- Potential Benefits of In Silico Methods: A Promising Alternative in Natural Compound's Drug Discovery and Repurposing for HBV Therapy.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Computational Landscape in Drug Discovery: From AI/ML Models to Translational Application.Scientifica · 2025Review
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.