Discovering the targets of drugs via computational systems biology.

J Biol Chem

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Published: July 2011

Computational systems biology is empowering the study of drug action. Studies on biological effects of chemical compounds have increased in scale and accessibility, allowing integration with other large-scale experimental data types. Here, we review computational approaches for elucidating the mechanisms of both intended and undesirable effects of drugs, with the collective potential to change the nature of drug discovery and pharmacological therapy.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129145PMC
http://dx.doi.org/10.1074/jbc.R110.174797DOI Listing

Publication Analysis

Top Keywords

computational systems
8
systems biology
8
discovering targets
4
targets drugs
4
drugs computational
4
biology computational
4
biology empowering
4
empowering study
4
study drug
4
drug action
4

Similar Publications

This paper systematically evaluates saliency methods as explainability tools for convolutional neural networks trained to diagnose glaucoma using simplified eye fundus images that contain only disc and cup outlines. These simplified images, a methodological novelty, were used to relate features highlighted in the saliency maps to the geometrical clues that experts consider in glaucoma diagnosis. Despite their simplicity, these images retained sufficient information for accurate classification, with balanced accuracies ranging from 0.

View Article and Find Full Text PDF

Learning the language of antibody hypervariability.

Proc Natl Acad Sci U S A

January 2025

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139.

Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose "foundational" PLMs have limited performance in modeling antibodies due to the latter's hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples.

View Article and Find Full Text PDF

Zoos must embrace animal death for education and conservation.

Proc Natl Acad Sci U S A

January 2025

Centre for Ecological Dynamics in a Novel Biosphere, Section of EcoInformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus 8000, Denmark.

View Article and Find Full Text PDF

As the global economy expands, waterway transportation has become increasingly crucial to the logistics sector. This growth presents both significant challenges and opportunities for enhancing the accuracy of ship detection and tracking through the application of artificial intelligence. This article introduces a multi-object tracking system designed for unmanned aerial vehicles (UAVs), utilizing the YOLOv7 and Deep SORT algorithms for detection and tracking, respectively.

View Article and Find Full Text PDF

Preterm births constitute a major public health issue and a chronic, cross-generational condition globally. Psychological and biological factors interact in a way that women from low socio-economic status (SES) are disproportionally affected by preterm delivery and at increased risk for the development of perinatal mental health problems. Low SES constitutes one of the most evident contributors to poor neurodevelopment of preterm infants.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!