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Drug Versioning and Legal Accountability for Preventable Product Harms.
JAMA
March 2025
Department of Chemistry, Dartmouth College, Hanover, New Hampshire.
Hypothesis generation for rare and undiagnosed diseases through clustering and classifying time-versioned biological ontologies.
PLoS One
December 2024
Department of Computer Science, University of Colorado Boulder, Boulder, CO, United States of America.
Rare diseases affect 1-in-10 people in the United States and despite increased genetic testing, up to half never receive a diagnosis. Even when using advanced genome sequencing platforms to discover variants, if there is no connection between the variants found in the patient's genome and their phenotypes in the literature, then the patient will remain undiagnosed. When a direct variant-phenotype connection is not known, putting a patient's information in the larger context of phenotype relationships and protein-protein interactions may provide an opportunity to find an indirect explanation.
View Article and Find Full Text PDFCombining crystallographic and binding affinity data towards a novel dataset of small molecule overlays.
J Comput Aided Mol Des
December 2024
University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany.
Although small molecule superposition is a standard technique in drug discovery, a rigorous performance assessment of the corresponding methods is currently challenging. Datasets in this field are sparse, small, tailored to specific applications, unavailable, or outdated. The newly developed LOBSTER set described herein offers a publicly available and method-independent dataset for benchmarking and method optimization.
View Article and Find Full Text PDFKG-Hub-building and exchanging biological knowledge graphs.
Bioinformatics
July 2023
Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
Motivation: Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking.
Results: Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects.
Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].
Living J Comput Mol Sci
August 2022
DeepCure, 131 Dartmouth St, Boston, MA 02116 USA.
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems () becomes critical to provide users with an assessment of the accuracy expected when these methods are applied within their domain of applicability, and developers with a way to assess the expected impact of new methodologies. These assessments require construction of a benchmark-a set of well-prepared, high quality systems with corresponding experimental measurements designed to ensure the resulting calculations provide a realistic assessment of expected performance when these methods are deployed within their domains of applicability.
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