Related references
Note: Only part of the references are listed.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)
Taba: A Tool to Analyze the Binding Affinity
Amauri Duarte da Silva et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2020)
Learning from the ligand: using ligand-based features to improve binding affinity prediction
Fergus Boyles et al.
BIOINFORMATICS (2020)
MathDL: mathematical deep learning for D3R Grand Challenge 4
Duc Duy Nguyen et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)
A Deep Learning Approach to Antibiotic Discovery
Jonathan M. Stokes et al.
CELL (2020)
Current Trends, Overlooked Issues, and Unmet Challenges in Virtual Screening
Dagmar Stumpfe et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Machine-learning scoring functions for structure-based drug lead optimization
Hongjian Li et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
Duc Duy Nguyen et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2019)
Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data
Hongjian Li et al.
BIOINFORMATICS (2019)
The next level in chemical space navigation: going far beyond enumerable compound libraries
Torsten Hoffmann et al.
DRUG DISCOVERY TODAY (2019)
Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning
Nobuaki Yasuo et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Ultra-large library docking for discovering new chemotypes
Jiankun Lyu et al.
NATURE (2019)
Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
Xin Yang et al.
CHEMICAL REVIEWS (2019)
AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening
Duc Duy Nguyen et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state
Pin Chen et al.
JOURNAL OF CHEMINFORMATICS (2019)
Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions
Jianing Lu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment
Hossam M. Ashtawy et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Virtual Screening in Hepatitis B Virus Drug Discovery: Current State-of-the-Art and Future Perspectives
Mohcine Elmessaoudi-Idrissi et al.
CURRENT MEDICINAL CHEMISTRY (2018)
Machine Learning Classification Models to Improve the Docking-based Screening: A Case of PI3K-Tankyrase Inhibitors
Vladimir P. Berishvili et al.
MOLECULAR INFORMATICS (2018)
Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets
Nathalie Lagarde et al.
Oncotarget (2018)
Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data
Fergus Imrie et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
The Impact of Protein Structure and Sequence Similarity on the Accuracy of Machine-Learning Scoring Functions for Binding Affinity Prediction
Hongjian Li et al.
BIOMOLECULES (2018)
The ChEMBL database in 2017
Anna Gaulton et al.
NUCLEIC ACIDS RESEARCH (2017)
Protein-Ligand Empirical Interaction Components for Virtual Screening
Yuna Yan et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Protein-Ligand Scoring with Convolutional Neural Networks
Matthew Ragoza et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Performance of machine-learning scoring functions in structure-based virtual screening
Maciej Wojcikowski et al.
SCIENTIFIC REPORTS (2017)
Building a virtual ligand screening pipeline using free software: a survey
Enrico Glaab
BRIEFINGS IN BIOINFORMATICS (2016)
Correcting the impact of docking pose generation error on binding affinity prediction
Hongjian Li et al.
BMC BIOINFORMATICS (2016)
USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques
Hongjian Li et al.
NUCLEIC ACIDS RESEARCH (2016)
Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization
Sakari Latti et al.
JOURNAL OF CHEMINFORMATICS (2016)
Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance
Ludovic Chaput et al.
JOURNAL OF CHEMINFORMATICS (2016)
Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery
Huiyong Sun et al.
SCIENTIFIC REPORTS (2016)
Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands
Jacob D. Durrant et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
Hierarchical virtual screening approaches in small molecule drug discovery
Ashutosh Kumar et al.
METHODS (2015)
Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets
Hongjian Li et al.
MOLECULAR INFORMATICS (2015)
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
Qurrat Ul Ain et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2015)
Does a More Precise Chemical Description of Protein-Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
Pedro J. Ballester et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Improvement of Virtual Screening Results by Docking Data Feature Analysis
Marcelino Arciniega et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
The holistic integration of virtual screening in drug discovery
Yusuf Tanrikulu et al.
DRUG DISCOVERY TODAY (2013)
Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0-A Public Library of Challenging Docking Benchmark Sets
Matthias R. Bauer et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
Douglas R. Houston et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise
David Ryan Koes et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Ligand Pose and Orientational Sampling in Molecular Docking
Ryan G. Coleman et al.
PLOS ONE (2013)
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
Michael M. Mysinger et al.
JOURNAL OF MEDICINAL CHEMISTRY (2012)
Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
Pedro J. Ballester et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2012)
Global Analysis of Small Molecule Binding to Related Protein Targets
Felix A. Kruger et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Structure-Based Virtual Screening Approach to the Discovery of Novel Inhibitors of Eyes Absent 2 Phosphatase with Various Metal Chelating Moieties
Hwangseo Park et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2011)
Support Vector Regression Scoring of Receptor-Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
Liwei Li et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Discovery of Potent Inhibitors of Soluble Epoxide Hydrolase by Combinatorial Library Design and Structure-Based Virtual Screening
Li Xing et al.
JOURNAL OF MEDICINAL CHEMISTRY (2011)
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
Pedro J. Ballester et al.
BIOINFORMATICS (2010)
Virtual screening: an endless staircase?
Gisbert Schneider
NATURE REVIEWS DRUG DISCOVERY (2010)
Fpocket: An open source platform for ligand pocket detection
Vincent Le Guilloux et al.
BMC BIOINFORMATICS (2009)
Mining free compound databases to identify candidates selected by virtual screening
Sridhar R. Vasudevan et al.
EXPERT OPINION ON DRUG DISCOVERY (2009)
Comparative Assessment of Scoring Functions on a Diverse Test Set
Tiejun Cheng et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Experimental Approaches to Evaluate the Thermodynamics of Protein- Drug Interactions
Walter Filgueira de Azevedo et al.
CURRENT DRUG TARGETS (2008)
UCSF chimera - A visualization system for exploratory research and analysis
EF Pettersen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Random forest: A classification and regression tool for compound classification and QSAR modeling
V Svetnik et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)
Molecular model of shikimate kinase from Mycobacterium tuberculosis
WF de Azevedo et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2002)
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B
TN Doman et al.
JOURNAL OF MEDICINAL CHEMISTRY (2002)