AIMC Topic: Software

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Rib fracture detection in computed tomography images using deep convolutional neural networks.

Medicine
To evaluate the rib fracture detection performance in computed tomography (CT) images using a software based on a deep convolutional neural network (DCNN) and compare it with the rib fracture diagnostic performance of doctors.We included CT images fr...

GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues.

Nucleic acids research
Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this pap...

State-of-the-art web services for de novo protein structure prediction.

Briefings in bioinformatics
Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent...

scCancer: a package for automated processing of single-cell RNA-seq data in cancer.

Briefings in bioinformatics
Molecular heterogeneities and complex microenvironments bring great challenges for cancer diagnosis and treatment. Recent advances in single-cell RNA-sequencing (scRNA-seq) technology make it possible to study cancer cell heterogeneities and microenv...

MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm.

Briefings in bioinformatics
Deep learning is an important branch of artificial intelligence that has been successfully applied into medicine and two-dimensional ligand design. The three-dimensional (3D) ligand generation in the 3D pocket of protein target is an interesting and ...

AntiCP 2.0: an updated model for predicting anticancer peptides.

Briefings in bioinformatics
Increasing use of therapeutic peptides for treating cancer has received considerable attention of the scientific community in the recent years. The present study describes the in silico model developed for predicting and designing anticancer peptides...

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.

Briefings in bioinformatics
DNA N4-methylcytosine (4mC) modification represents a novel epigenetic regulation. It involves in various cellular processes, including DNA replication, cell cycle and gene expression, among others. In addition to experimental identification of 4mC s...

MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery.

Bioinformatics (Oxford, England)
MOTIVATION: Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, drug repurposing and uncovering off-target effects. Due to the tremendous size of the chemical space, experimental b...

Predicting candidate genes from phenotypes, functions and anatomical site of expression.

Bioinformatics (Oxford, England)
MOTIVATION: Over the past years, many computational methods have been developed to incorporate information about phenotypes for disease-gene prioritization task. These methods generally compute the similarity between a patient's phenotypes and a data...

A novel sequence alignment algorithm based on deep learning of the protein folding code.

Bioinformatics (Oxford, England)
MOTIVATION: From evolutionary interference, function annotation to structural prediction, protein sequence comparison has provided crucial biological insights. While many sequence alignment algorithms have been developed, existing approaches often ca...