4.7 Article

BEAR: A Novel Virtual Screening Method Based on Large-Scale Bioactivity Data

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Comparative Toxicogenomics Database (CTD): update 2021

Allan Peter Davis et al.

Summary: The public Comparative Toxicogenomics Database (CTD) is a digital ecosystem that integrates toxicological information to advance understanding about human health. With a 20% increase in curated content, CTD now provides an extensive dataset for over 16,300 chemicals, 51,300 genes, and more, enhancing its usefulness as a resource for generating testable hypotheses about environmentally influenced diseases.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction

Niraj Verma et al.

Summary: This study introduces a DNN framework called SSnet, which utilizes protein secondary structure information to predict PLI, and compares its performance with other machine and non-machine learning models. The results show that SSnet learns information related to ligand binding in proteins and is not restricted by molecular conformation. SSnet extracts critical protein folding information for PLI prediction.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Biochemistry & Molecular Biology

Deep Learning in Virtual Screening: Recent Applications and Developments

Talia B. Kimber et al.

Summary: Machine learning plays a crucial role in drug discovery, especially in virtual screening, with a focus on deep learning techniques. Recent research mainly focuses on different compound and protein encodings, as well as data sets used for model training and testing.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Pharmacology & Pharmacy

Clinically-Relevant ABC Transporter for Anti-Cancer Drug Resistance

Huan Xiao et al.

Summary: This review summarizes the recent advances in important cancer-related ABC transporters, focusing on their physiological functions, structures, and the development of new compounds as ABC transporter inhibitors, highlighting the potential use of modulators to enhance the therapeutic efficacy of chemotherapy drugs.

FRONTIERS IN PHARMACOLOGY (2021)

Article Pharmacology & Pharmacy

Dual Inhibition of P-gp and BCRP Improves Oral Topotecan Bioavailability in Rodents

Jaeok Lee et al.

Summary: The inhibition of P-gp and BCRP by natural derivatives has shown promise in overcoming multidrug resistance in cancer chemotherapy, increasing the bioavailability of anticancer drugs and reducing drug resistance in cells. This approach could potentially be a useful clinical strategy.

PHARMACEUTICS (2021)

Review Biochemistry & Molecular Biology

Comprehensive Survey of Recent Drug Discovery Using Deep Learning

Jintae Kim et al.

Summary: Drug discovery based on artificial intelligence reduces time and cost, with challenges in predicting drug-target interactions and generating novel molecular structures. Recent research focuses on drug-target interaction prediction and de novo drug design.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Review Chemistry, Multidisciplinary

From machine learning to deep learning: Advances in scoring functions for protein-ligand docking

Chao Shen et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)

Review Chemistry, Multidisciplinary

Machine-learning scoring functions for structure-based drug lead optimization

Hongjian Li et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)

Article Chemistry, Multidisciplinary

CSgator: an integrated web platform for compound set analysis

Sera Park et al.

JOURNAL OF CHEMINFORMATICS (2019)

Article Biotechnology & Applied Microbiology

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

Alex Zhavoronkov et al.

NATURE BIOTECHNOLOGY (2019)

Article Chemistry, Medicinal

Comparative Assessment of Scoring Functions: The CASF-2016 Update

Minyi Su et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Biochemistry & Molecular Biology

ChEMBL: towards direct deposition of bioassay data

David Mendez et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Biochemistry & Molecular Biology

Current computational methods for predicting protein interactions of natural products

Aurelien F. A. Moumbock et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2019)

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Pharmacology & Pharmacy

QSAR-Based Virtual Screening: Advances and Applications in Drug Discovery

Bruno J. Neves et al.

FRONTIERS IN PHARMACOLOGY (2018)

Article Biochemistry & Molecular Biology

The ChEMBL database in 2017

Anna Gaulton et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

PubChem BioAssay: 2017 update

Yanli Wang et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Multidisciplinary

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

Jiangming Sun et al.

JOURNAL OF CHEMINFORMATICS (2017)

Review Biochemistry & Molecular Biology

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

Elizabeth Yuriev et al.

JOURNAL OF MOLECULAR RECOGNITION (2015)

Article Biochemistry & Molecular Biology

The ChEMBL bioactivity database: an update

A. Patricia Bento et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

Scaffold network generator: a tool for mining molecular structures

Matt K. Matlock et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Rethinking Molecular Similarity: Comparing Compounds on the Basis of Biological Activity

Faula M. Petrone et al.

ACS CHEMICAL BIOLOGY (2012)

Article Chemistry, Medicinal

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

Michael M. Mysinger et al.

JOURNAL OF MEDICINAL CHEMISTRY (2012)

Article Chemistry, Multidisciplinary

Open Babel: An open chemical toolbox

Noel M. O'Boyle et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Multidisciplinary Sciences

Discovery of drug mode of action and drug repositioning from transcriptional responses

Francesco Iorio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Chemistry, Multidisciplinary

Efficient Drug Lead Discovery and Optimization

William L. Jorgensen

ACCOUNTS OF CHEMICAL RESEARCH (2009)

Review Biochemical Research Methods

Recent advances in computer-aided drug design

Chun Meng Song et al.

BRIEFINGS IN BIOINFORMATICS (2009)

Article Chemistry, Medicinal

Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data

Sebastian G. Rohrer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)

Article Biochemistry & Molecular Biology

SuperTarget and Matador: resources for exploring drug-target relationships

Stefan Guenther et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Binding MOAD, a high-quality protein-ligand database

Mark L. Benson et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Biochemistry & Molecular Biology

Virtual screening strategies in drug discovery

Campbell McInnes

CURRENT OPINION IN CHEMICAL BIOLOGY (2007)

Review Pharmacology & Pharmacy

Origin and evolution of high throughput screening

D. A. Pereira et al.

BRITISH JOURNAL OF PHARMACOLOGY (2007)

Review Biotechnology & Applied Microbiology

Integration of virtual and high-throughput screening

F Bajorath

NATURE REVIEWS DRUG DISCOVERY (2002)

Article Biochemistry & Molecular Biology

TTD: Therapeutic Target Database

X Chen et al.

NUCLEIC ACIDS RESEARCH (2002)