AIMC Topic: Software

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Deep learning-based denoising for unbiased analysis of morphology and stiffness in amyloid fibrils.

Computers in biology and medicine
Understanding the morphology of amyloid fibrils is crucial for comprehending the aggregation and degradation mechanisms of abnormal proteins implicated in various diseases, such as Alzheimer's disease, Parkinson's disease, type II diabetes, and vario...

Accurate RNA 3D structure prediction using a language model-based deep learning approach.

Nature methods
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The stru...

Artificial intelligence contouring in radiotherapy for organs-at-risk and lymph node areas.

Radiation oncology (London, England)
INTRODUCTION: The delineation of organs-at-risk and lymph node areas is a crucial step in radiotherapy, but it is time-consuming and associated with substantial user-dependent variability in contouring. Artificial intelligence (AI) appears to be the ...

MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning.

Journal of molecular biology
Multi-ligand binding residues (MLBRs) are amino acids in protein sequences that interact with multiple different ligands that include proteins, peptides, nucleic acids, and a variety of small molecules. MLBRs are implicated in a number of cellular fu...

Quantifying the Scope of Artificial Intelligence-Assisted Writing in Orthopaedic Medical Literature: An Analysis of Prevalence and Validation of AI-Detection Software.

The Journal of the American Academy of Orthopaedic Surgeons
INTRODUCTION: The popularization of generative artificial intelligence (AI), including Chat Generative Pre-trained Transformer (ChatGPT), has raised concerns for the integrity of academic literature. This study asked the following questions: (1) Has ...

PredIDR: Accurate prediction of protein intrinsic disorder regions using deep convolutional neural network.

International journal of biological macromolecules
The involvement of protein intrinsic disorder in essential biological processes, it is well known in structural biology. However, experimental methods for detecting intrinsic structural disorder and directly measuring highly dynamic behavior of prote...

Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning.

Nature methods
While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the 'preferred' orientation problem) remains a complication for most specimens. Existing ...

vScreenML v2.0: Improved Machine Learning Classification for Reducing False Positives in Structure-Based Virtual Screening.

International journal of molecular sciences
The enthusiastic adoption of make-on-demand chemical libraries for virtual screening has highlighted the need for methods that deliver improved hit-finding discovery rates. Traditional virtual screening methods are often inaccurate, with most compoun...

Analysis of solid-state NMR data facilitated by MagRO_NMRViewJ with Graph_Robot: Application for membrane protein and amyloid.

Biophysical chemistry
Solid-state NMR (ssNMR) methods have continued to be developed in recent years for the efficient assignment of signals and 3D structure modeling of biomacromolecules. Consequently, we are approaching an era in which vigorous applications of these met...

Multi-Institutional Evaluation and Training of Breast Density Classification AI Algorithm Using ACR Connect and AI-LAB.

Journal of the American College of Radiology : JACR
OBJECTIVE: To demonstrate and test the capabilities of the ACR Connect and AI-LAB software platform by implementing multi-institutional artificial intelligence (AI) training and validation for breast density classification.