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SPONGE-FEP: An Automated Relative Binding Free Energy Calculation Accelerated by Selective Integrated Tempering Sampling.
J Chem Theory Comput
January 2025
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
Computer-aided drug discovery (CADD) utilizes computational methods to accelerate the identification and optimization of potential drug candidates. Free energy perturbation (FEP) and thermodynamic integration (TI) play a critical role in predicting differences in protein binding affinities between drug molecules. Here, we implement SPONGE-FEP, which incorporates selective integrated tempering sampling (SITS) to enhance sampling efficiency and contains an automated workflow for relative binding free energy (RBFE) calculations.
View Article and Find Full Text PDFExamining hurricane-related social media topics longitudinally and at scale: A transformer-based approach.
PLoS One
January 2025
Computational Media Lab, University of Texas at Austin, Austin, Texas, United States of America.
Instead of turning to emergency phone systems, social media platforms, such as Twitter, have emerged as alternative and sometimes preferred venues for members of the public in the US to communicate during hurricanes and other natural disasters. However, relevant posts are likely to be missed by responders given the volume of content on platforms. Previous work successfully identified relevant posts through machine-learned methods, but depended on human annotators.
View Article and Find Full Text PDFIntroducing GPU Acceleration into the Python-Based Simulations of Chemistry Framework.
J Phys Chem A
January 2025
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.
We introduce the first version of GPU4PySCF, a module that provides GPU acceleration of methods in PySCF. As a core functionality, this provides a GPU implementation of two-electron repulsion integrals (ERIs) for contracted basis sets comprising up to functions using the Rys quadrature. As an illustration of how this can accelerate a quantum chemistry workflow, we describe how to use the ERIs efficiently in the integral-direct Hartree-Fock build and nuclear gradient construction.
View Article and Find Full Text PDFUltra-high-resolution brain MRI at 0.55T: bSTAR and its application to magnetization transfer ratio imaging.
Z Med Phys
January 2025
Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Department of Radiology, Division of Radiological Physics, University Hospital Basel, Basel, Switzerland.
Purpose: This study aims to evaluate the feasibility of structural sub-millimeter isotropic brain MRI at 0.55 T using a 3D half-radial dual-echo balanced steady-state free precession sequence, termed bSTAR and to assess its potential for high-resolution magnetization transfer imaging.
Methods: Phantom and in-vivo imaging of three healthy volunteers was performed on a low-field 0.
HCTTI: High-Performance Heterogeneous Computing Toolkit for Tissue Image Stain Normalization.
J Imaging Inform Med
January 2025
Department of Pathology, Sinopharm Tongmei General Hospital, Datong, 037003, Shanxi, China.
Whole slide imaging (WSI) has transformed diagnostic medicine, particularly in the field of cancer diagnosis and treatment. The use of deep learning algorithms for predicting WSIs has opened up new avenues for advanced medical diagnostics. Additionally, stain normalization can reduce the color and intensity variations present in WSI from different hospitals.
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