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LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds

期刊: JOURNAL OF CHEMINFORMATICS, 2021; 13 (1)

Target prediction is a crucial step in modern drug discovery. However, existing experimental approaches to target prediction are time-consuming and co......

Multi-PLI: interpretable multi-task deep learning model for unifying protein-ligand interaction datasets

期刊: JOURNAL OF CHEMINFORMATICS, 2021; 13 (1)

The assessment of protein-ligand interactions is critical at early stage of drug discovery. Computational approaches for efficiently predicting such i......

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions

期刊: JOURNAL OF CHEMINFORMATICS, 2021; 13 (1)

Virtual screening (VS) based on molecular docking has emerged as one of the mainstream technologies of drug discovery due to its low cost and high eff......

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

期刊: JOURNAL OF CHEMINFORMATICS, 2021; 13 (1)

Protein solubility is significant in producing new soluble proteins that can reduce the cost of biocatalysts or therapeutic agents. Therefore, a compu......

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models

期刊: JOURNAL OF CHEMINFORMATICS, 2021; 13 (1)

Graph neural networks (GNN) has been considered as an attractive modelling method for molecular property prediction, and numerous studies have shown t......

Neural machine translation of chemical nomenclature between English and Chinese

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Machine translation of chemical nomenclature has considerable application prospect in chemical text data processing between languages. However, rule b......

Memory-assisted reinforcement learning for diverse molecular de novo design

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

In de novo molecular design, recurrent neural networks (RNN) have been shown to be effective methods for sampling and generating novel chemical struct......

Building attention and edge message passing neural networks for bioactivity and physical-chemical property prediction

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Neural Message Passing for graphs is a promising and relatively recent approach for applying Machine Learning to networked data. As molecules can be d......

ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Breast cancer resistance protein (BCRP/ABCG2), an ATP-binding cassette (ABC) efflux transporter, plays a critical role in multi-drug resistance (MDR) ......

The diatomic molecular spectroscopy database

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Motivation The spectroscopy of diatomic molecules is an important research area in chemical physics due to its relevance in astrochemistry, combustion......

SMILES-based deep generative scaffold decorator for de-novo drug design

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Molecular generative models trained with small sets of molecules represented as SMILES strings can generate large regions of the chemical space. Unfor......

Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

With the rise of artificial intelligence (AI) in drug discovery, de novo molecular generation provides new ways to explore chemical space. However, be......

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Background The increasing number of organic and inorganic structures promotes the development of the "Big Data" in chemistry and material science, and......

Structure-activity relationship-based chemical classification of highly imbalanced Tox21 datasets

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in......

A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility

期刊: JOURNAL OF CHEMINFORMATICS, 2020; 12 (1)

Efficient and accurate prediction of molecular properties, such as lipophilicity and solubility, is highly desirable for rational compound design in c......

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