Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

(2019) Jochen Sieg et al.   Journal of Chemical Information and Modeling

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

Design, synthesis and biological evaluation of pyrimidine derivatives as novel CDK2 inhibitors that induce apoptosis and cell cycle arrest in breast cancer cells

(2018) Yiting Wang et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Visualizing convolutional neural network protein-ligand scoring

(2018) Joshua Hochuli et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Activity and selectivity cliffs for DPP-IV inhibitors: Lessons we can learn from SAR studies and their application to virtual screening

(2018) María José Ojeda-Montes et al.   MEDICINAL RESEARCH REVIEWS

Machine Learning Classification Models to Improve the Docking-based Screening: A Case of PI3K-Tankyrase Inhibitors

(2018) Vladimir P. Berishvili et al.   Molecular Informatics

Improving Docking Performance Using Negative Image-Based Rescoring

(2018) Sami T. Kurkinen et al.   Frontiers in Pharmacology

Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data

(2018) Fergus Imrie et al.   Journal of Chemical Information and Modeling

Protein–Ligand Empirical Interaction Components for Virtual Screening

(2017) Yuna Yan et al.   Journal of Chemical Information and Modeling

Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening

(2017) Spencer S. Ericksen et al.   Journal of Chemical Information and Modeling

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Boosting Docking-Based Virtual Screening with Deep Learning

(2016) Janaina Cruz Pereira et al.   Journal of Chemical Information and Modeling

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

(2016) Ludovic Chaput et al.   Journal of Cheminformatics

Function-specific virtual screening for GPCR ligands using a combined scoring method

(2016) Albert J. Kooistra et al.   Scientific Reports

TS-Chemscore, a Target-Specific Scoring Function, Significantly Improves the Performance of Scoring in Virtual Screening

(2014) Wen-Jing Wang et al.   Chemical Biology & Drug Design

From Laptop to Benchtop to Bedside: Structure-based Drug Design on Protein Targets

(2012) Lu Chen et al.   CURRENT DRUG METABOLISM

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

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation

(2011) Liwei Li et al.   Journal of Chemical Information and Modeling

Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions

(2010) Mengzhu Xue et al.   Journal of Chemical Information and Modeling

Structure-Based Drug Design Strategies in Medicinal Chemistry

(2009) Adriano Andricopulo et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Consensus Scoring with Feature Selection for Structure-Based Virtual Screening

(2008) Reiji Teramoto et al.   Journal of Chemical Information and Modeling

Recommendations for evaluation of computational methods

(2008) Ajay N. Jain et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

2-Amino-6-furan-2-yl-4-substituted Nicotinonitriles as A2AAdenosine Receptor Antagonists

(2008) Monica Mantri et al.   JOURNAL OF MEDICINAL CHEMISTRY