Motivation: A single-precision value is currently reported for an integrative model. However, precision may vary for different regions of an integrative model owing to varying amounts of input information.
Results: We develop PrISM (Precision for Integrative Structural Models) to efficiently identify high- and low-precision regions for integrative models.
Availability And Implementation: PrISM is written in Python and available under the GNU General Public License v3.0 at https://github.com/isblab/prism; benchmark data used in this paper are available at doi:10.5281/zenodo.6241200.
Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btac400 | DOI Listing |
Front Immunol
January 2025
Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität of Würzburg, Würzburg, Germany.
Background: The immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It is highly dynamic and reflects the current cellular state, enabling the immune system to recognize abnormal cellular conditions, such as those present in cancer cells. To precisely determine how changes in cellular processes, such as those induced by drug treatment, affect the immunopeptidome, quantitative immunopeptidomics approaches are essential.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Buk-gu, Gwangju 61005, Republic of Korea.
Combination therapies have emerged as a promising approach for treating complex diseases, particularly cancer. However, predicting the efficacy and safety profiles of these therapies remains a significant challenge, primarily because of the complex interactions among drugs and their wide-ranging effects. To address this issue, we introduce DD-PRiSM (Decomposition of Drug-Pair Response into Synergy and Monotherapy effect), a deep-learning pipeline that predicts the effects of combination therapy.
View Article and Find Full Text PDFRetin Cases Brief Rep
October 2024
Singapore National Eye Centre, Singapore.
Purpose: We describe an atypical presentation of an 11-year-old female with enhanced S-cone syndrome (ESCS).
Methods: Case report. The patient underwent a thorough ophthalmic examination and investigations such as colour fundus photography, optical coherence tomography, fundus autofluorescence, fluorescein and indocyanine angiography, an electroretinogram and genetic testing.
Acc Chem Res
January 2025
Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
ConspectusStructural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures.
View Article and Find Full Text PDFACS Omega
December 2024
Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México.
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