AIMC Topic: Software

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DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization.

Journal of chemical information and modeling
Lead optimization, a critical step in early stage drug discovery, involves making chemical modifications to a small-molecule ligand to improve properties such as binding affinity. We recently developed DeepFrag, a deep-learning model capable of recom...

Deep Learning-Based Advances in Protein Structure Prediction.

International journal of molecular sciences
Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine prot...

DeepD2V: A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence.

International journal of molecular sciences
Predicting in vivo protein-DNA binding sites is a challenging but pressing task in a variety of fields like drug design and development. Most promoters contain a number of transcription factor (TF) binding sites, but only a small minority has been id...

DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method.

International journal of molecular sciences
It is essential for future research to develop a new, reliable prediction method of DNA binding sites because DNA binding sites on DNA-binding proteins provide critical clues about protein function and drug discovery. However, the current prediction ...

Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets.

Nature communications
Understanding the structural determinants of a protein's biochemical properties, such as activity and stability, is a major challenge in biology and medicine. Comparing computer simulations of protein variants with different biochemical properties is...

XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties.

Journal of chemical information and modeling
Determining the properties of chemical molecules is essential for screening candidates similar to a specific drug. These candidate molecules are further evaluated for their target binding affinities, side effects, target missing probabilities, etc. C...

Artificial neural networks in tandem with molecular descriptors as predictive tools for continuous liposome manufacturing.

International journal of pharmaceutics
The current study utilized an artificial neural network (ANN) to generate computational models to achieve process optimization for a previously developed continuous liposome manufacturing system. The liposome formation was based on a continuous manuf...

A Deep Learning Enhanced Novel Software Tool for Laryngeal Dynamics Analysis.

Journal of speech, language, and hearing research : JSLHR
Purpose High-speed videoendoscopy (HSV) is an emerging, but barely used, endoscopy technique in the clinic to assess and diagnose voice disorders because of the lack of dedicated software to analyze the data. HSV allows to quantify the vocal fold osc...

Treasuring the computational approach in medicinal plant research.

Progress in biophysics and molecular biology
Medicinal plants serve as a valuable source of secondary metabolites since time immemorial. Computational Research in 21st century is giving more attention to medicinal plants for new drug design as pharmacological screening of bioactive compound was...

Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing.

Annual review of biomedical data science
The COVID-19 (coronavirus disease 2019) pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread. Many of these difficulties are fund...