ArticleJournal of computer-aided molecular design
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery.
Article in Journal of computer-aided molecular design. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment.Molecules (Basel, Switzerland) · 2017Pooled it
- DrugGym: A testbed for the economics of autonomous drug discovery.bioRxiv : the preprint server for biology · 2024Article
- Combatting over-specialization bias in growing chemical databases.Journal of cheminformatics · 2023Article
- Digitizing chemical discovery with a Bayesian explorer for interpreting reactivity data.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study.Journal of cheminformatics · 2021Article
- Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design.Journal of chemical information and modeling · 2020Article
- Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.Journal of computer-aided molecular design · 2019Article
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- Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose.Journal of computer-aided molecular design · 2018Article
- Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis.Journal of chemical information and modeling · 2018Article
- Decoys Selection in Benchmarking Datasets: Overview and Perspectives.Frontiers in pharmacology · 2018Review
- A Simple Representation of Three-Dimensional Molecular Structure.Journal of medicinal chemistry · 2017Article
- Validated UPLC-MS/MS method for the determination of tadalafil in human plasma and its application to a pharmacokinetic study.Translational and clinical pharmacology · 2017Article
- Computational analysis reveal inhibitory action of nimbin against dengue viral envelope protein.Virusdisease · 2015Article
- Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock.Journal of computer-aided molecular design · 2015Article
- Comparative modeling and benchmarking data sets for human histone deacetylases and sirtuin families.Journal of chemical information and modeling · 2015Article
- Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.Methods (San Diego, Calif.) · 2015Article
- Prediction of off-target drug effects through data fusion.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2014Article
- Surflex-Dock: Docking benchmarks and real-world application.Journal of computer-aided molecular design · 2012Article
- Does your model weigh the same as a duck?Journal of computer-aided molecular design · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Inductive bias is the set of assumptions that a person or procedure makes in making a prediction based on data. Different methods for ligand-based predictive modeling have different inductive biases, with a particularly sharp contrast between 2D and 3D similarity methods. A unique aspect of ligand design is that the data that exist to test methodology have been largely man-made, and that this process of design involves prediction. By analyzing the molecular similarities of known drugs, we show that the inductive bias of the historic drug discovery process has a very strong 2D bias. In studying the performance of ligand-based modeling methods, it is critical to account for this issue in dataset preparation, use of computational controls, and in the interpretation of results. We propose specific strategies to explicitly address the problems posed by inductive bias considerations.
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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.