标题
A practical guide to machine-learning scoring for structure-based virtual screening
作者
关键词
-
出版物
Nature Protocols
Volume 18, Issue 11, Pages 3460-3511
出版商
Springer Science and Business Media LLC
发表日期
2023-10-16
DOI
10.1038/s41596-023-00885-w
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor
- (2023) Feng Ren et al. Chemical Science
- Beware of Simple Methods for Structure-Based Virtual Screening: The Critical Importance of Broader Comparisons
- (2023) Viet-Khoa Tran-Nguyen et al. Journal of Chemical Information and Modeling
- On the Best Way to Cluster NCI-60 Molecules
- (2023) Saiveth Hernández-Hernández et al. Biomolecules
- Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses
- (2022) Andreas Luttens et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking
- (2022) Francesco Gentile et al. Nature Protocols
- Screening ultra-large virtual libraries
- (2022) Sarah Crunkhorn NATURE REVIEWS DRUG DISCOVERY
- What's next for AlphaFold and the AI protein-folding revolution
- (2022) Ewen Callaway NATURE
- HEBO: An Empirical Study of Assumptions in Bayesian Optimisation
- (2022) Alexander I. Cowen-Rivers et al. JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH
- Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery
- (2022) Felix Wong et al. Molecular Systems Biology
- NMR-Based Methods for Protein Analysis
- (2021) Yunfei Hu et al. ANALYTICAL CHEMISTRY
- Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?
- (2021) Chao Shen et al. BRIEFINGS IN BIOINFORMATICS
- Property-Unmatched Decoys in Docking Benchmarks
- (2021) Reed M. Stein et al. Journal of Chemical Information and Modeling
- A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening
- (2021) Christoph Gorgulla et al. iScience
- Generating property-matched decoy molecules using deep learning
- (2021) Fergus Imrie et al. BIOINFORMATICS
- Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations
- (2021) Gert-Jan Bekker et al. Scientific Reports
- Persistent spectral–based machine learning (PerSpect ML) for protein-ligand binding affinity prediction
- (2021) Zhenyu Meng et al. Science Advances
- True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better
- (2021) Viet-Khoa Tran-Nguyen et al. Journal of Chemical Information and Modeling
- Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses
- (2021) Fergus Boyles et al. Journal of Chemical Information and Modeling
- Highly accurate protein structure prediction with AlphaFold
- (2021) John Jumper et al. NATURE
- GNINA 1.0: molecular docking with deep learning
- (2021) Andrew T. McNutt et al. Journal of Cheminformatics
- Featurization strategies for protein–ligand interactions and their applications in scoring function development
- (2021) Guoli Xiong et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design
- (2021) Peiran Jiang et al. BRIEFINGS IN BIOINFORMATICS
- Recent progress on the prospective application of machine learning to structure-based virtual screening
- (2021) Ghita Ghislat et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Virtual Screening with Gnina 1.0
- (2021) Jocelyn Sunseri et al. MOLECULES
- A practical guide to large-scale docking
- (2021) Brian J. Bender et al. Nature Protocols
- Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)
- (2021) Xudong Wu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells
- (2021) Zechen Wang et al. Frontiers in Chemistry
- A Deep Learning Approach to Antibiotic Discovery
- (2020) Jonathan M. Stokes et al. CELL
- Virtual discovery of melatonin receptor ligands to modulate circadian rhythms
- (2020) Reed M. Stein et al. NATURE
- Revolutionary cryo-EM is taking over structural biology
- (2020) Ewen Callaway NATURE
- Machine‐learning scoring functions for structure‐based drug lead optimization
- (2020) Hongjian Li et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening
- (2020) Viet-Khoa Tran-Nguyen et al. Journal of Chemical Information and Modeling
- An open-source drug discovery platform enables ultra-large virtual screens
- (2020) Christoph Gorgulla et al. NATURE
- Machine‐learning scoring functions for structure‐based virtual screening
- (2020) Hongjian Li et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity
- (2020) Mariama Jaiteh et al. PLoS Computational Biology
- graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes
- (2020) Dmitry S. Karlov et al. ACS Omega
- The impact of compound library size on the performance of scoring functions for structure-based virtual screening
- (2020) Louison Fresnais et al. BRIEFINGS IN BIOINFORMATICS
- Improving structure-based virtual screening performance via learning from scoring function components
- (2020) Guo-Li Xiong et al. BRIEFINGS IN BIOINFORMATICS
- Bayer’s in silico ADMET platform: a journey of machine learning over the past two decades
- (2020) Andreas H. Göller et al. DRUG DISCOVERY TODAY
- Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement
- (2020) Viet-Khoa Tran-Nguyen et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Discovery of Novel Inhibitors of a Critical Brain Enzyme Using a Homology Model and a Deep Convolutional Neural Network
- (2020) Adrian Stecula et al. JOURNAL OF MEDICINAL CHEMISTRY
- Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding
- (2020) Kevin McCloskey et al. JOURNAL OF MEDICINAL CHEMISTRY
- Machine learning classification can reduce false positives in structure-based virtual screening
- (2020) Yusuf O. Adeshina et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Generating multibillion chemical space of readily accessible screening compounds
- (2020) Oleksandr O. Grygorenko et al. iScience
- Extended connectivity interaction features: improving binding affinity prediction through chemical description
- (2020) Norberto Sánchez-Cruz et al. BIOINFORMATICS
- ‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures
- (2020) Ewen Callaway NATURE
- A method for validating the accuracy of NMR protein structures
- (2020) Nicholas J. Fowler et al. Nature Communications
- Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters
- (2019) Conrad Stork et al. Journal of Chemical Information and Modeling
- Bigger is better in virtual drug screens
- (2019) David E. Gloriam NATURE
- Ultra-large library docking for discovering new chemotypes
- (2019) Jiankun Lyu et al. NATURE
- Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning
- (2019) Nobuaki Yasuo et al. Journal of Chemical Information and Modeling
- Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data
- (2019) Hongjian Li et al. BIOINFORMATICS
- Homology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III
- (2019) Saroj Kumar Panda et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- From machine learning to deep learning: Advances in scoring functions for protein-ligand docking
- (2019) Chao Shen et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- NERDD: a web portal providing access to in silico tools for drug discovery
- (2019) Conrad Stork et al. BIOINFORMATICS
- Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods
- (2019) Dingyan Wang et al. Frontiers in Pharmacology
- A drug-likeness toolbox facilitates ADMET study in drug discovery
- (2019) Chen-Yang Jia et al. DRUG DISCOVERY TODAY
- MathDL: mathematical deep learning for D3R Grand Challenge 4
- (2019) Duc Duy Nguyen et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Development and evaluation of a deep learning model for protein–ligand binding affinity prediction
- (2018) Marta M Stepniewska-Dziubinska et al. BIOINFORMATICS
- Cryptic binding sites on proteins: definition, detection, and druggability
- (2018) Sandor Vajda et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization
- (2018) Izhar Wallach et al. Journal of Chemical Information and Modeling
- MoleculeNet: a benchmark for molecular machine learning
- (2018) Zhenqin Wu et al. Chemical Science
- Mordred: a molecular descriptor calculator
- (2018) Hirotomo Moriwaki et al. Journal of Cheminformatics
- Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
- (2018) Zixuan Cang et al. PLoS Computational Biology
- Decoys Selection in Benchmarking Datasets: Overview and Perspectives
- (2018) Manon Réau et al. Frontiers in Pharmacology
- Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions
- (2018) Maciej Wójcikowski et al. BIOINFORMATICS
- Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
- (2018) Duc Duy Nguyen et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- 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
- Practical Model Selection for Prospective Virtual Screening
- (2018) Shengchao Liu et al. Journal of Chemical Information and Modeling
- All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening
- (2018) Viet-Khoa Tran-Nguyen et al. Journal of Chemical Information and Modeling
- ChEMBL: towards direct deposition of bioassay data
- (2018) David Mendez et al. NUCLEIC ACIDS RESEARCH
- Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril
- (2018) Jie Zhu et al. Scientific Reports
- Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment
- (2017) Hossam M. Ashtawy 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
- Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS
- (2017) Stephen J. Capuzzi et al. Journal of Chemical Information and Modeling
- Comment on The Ecstasy and Agony of Assay Interference Compounds
- (2017) Peter W. Kenny Journal of Chemical Information and Modeling
- PDBe: towards reusable data delivery infrastructure at protein data bank in Europe
- (2017) Saqib Mir et al. NUCLEIC ACIDS RESEARCH
- Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models
- (2017) Abba E. Leffler et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Homology Modeling and Virtual Screening to Discover Potent Inhibitors Targeting the Imidazole Glycerophosphate Dehydratase Protein in Staphylococcus xylosus
- (2017) Xing-Ru Chen et al. Frontiers in Chemistry
- PubChem BioAssay: A Decade’s Development toward Open High-Throughput Screening Data Sharing
- (2017) Yanli Wang et al. SLAS Discovery
- Performance of machine-learning scoring functions in structure-based virtual screening
- (2017) Maciej Wójcikowski et al. Scientific Reports
- Review: The HSP90 molecular chaperone-an enigmatic ATPase
- (2016) Laurence H. Pearl BIOPOLYMERS
- Correcting the impact of docking pose generation error on binding affinity prediction
- (2016) Hongjian Li et al. BMC BIOINFORMATICS
- Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest
- (2016) Cheng Wang et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Highly Promiscuous Small Molecules from Biological Screening Assays Include Many Pan-Assay Interference Compounds but Also Candidates for Polypharmacology
- (2016) Erik Gilberg et al. JOURNAL OF MEDICINAL CHEMISTRY
- Feeling Nature’s PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS)
- (2016) Jonathan B. Baell JOURNAL OF NATURAL PRODUCTS
- Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations
- (2016) Vladimiras Oleinikovas et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The SWISS-MODEL Repository—new features and functionality
- (2016) Stefan Bienert et al. NUCLEIC ACIDS RESEARCH
- Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery
- (2016) Huiyong Sun et al. Scientific Reports
- Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins
- (2015) Hossam M Ashtawy et al. BMC BIOINFORMATICS
- Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands
- (2015) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives
- (2015) Nathalie Lagarde et al. Journal of Chemical Information and Modeling
- Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets
- (2015) Hongjian Li et al. Molecular Informatics
- SureChEMBL: a large-scale, chemically annotated patent document database
- (2015) George Papadatos et al. NUCLEIC ACIDS RESEARCH
- Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
- (2015) Qurrat Ul Ain et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets
- (2015) Takaya Saito et al. PLoS One
- Integrating docking scores, interaction profiles and molecular descriptors to improve the accuracy of molecular docking: Toward the discovery of novel Akt1 inhibitors
- (2014) Wenhu Zhan et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
- (2014) Pedro J. Ballester et al. Journal of Chemical Information and Modeling
- Applicability Domain Based on Ensemble Learning in Classification and Regression Analyses
- (2014) Hiromasa Kaneko et al. Journal of Chemical Information and Modeling
- Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study
- (2014) C. Da et al. Journal of Chemical Information and Modeling
- Applicability Domain Analysis (ADAN): A Robust Method for Assessing the Reliability of Drug Property Predictions
- (2014) Pau Carrió et al. Journal of Chemical Information and Modeling
- Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
- (2014) Stefan Bietz et al. Journal of Cheminformatics
- Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison
- (2014) Vladimir Chupakhin et al. Computational and Structural Biotechnology Journal
- Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets
- (2013) Matthias R. Bauer et al. Journal of Chemical Information and Modeling
- Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL
- (2013) Tomasz Makarewicz et al. Journal of Chemical Information and Modeling
- Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise
- (2013) David Ryan Koes et al. Journal of Chemical Information and Modeling
- Applicability Domain Dependent Predictive Uncertainty in QSAR Regressions
- (2013) U. Sahlin et al. Molecular Informatics
- Ligand Pose and Orientational Sampling in Molecular Docking
- (2013) Ryan G. Coleman et al. PLoS One
- Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase
- (2013) Abdelmonaem Messaoudi et al. Theoretical Biology and Medical Modelling
- On the Value of Homology Models for Virtual Screening: Discovering hCXCR3 Antagonists by Pharmacophore-Based and Structure-Based Approaches
- (2012) Dane Huang et al. Journal of Chemical Information and Modeling
- ZINC: A Free Tool to Discover Chemistry for Biology
- (2012) John J. Irwin et al. Journal of Chemical Information and Modeling
- A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
- (2012) Marc van Dijk et al. Journal of Chemical Theory and Computation
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
- (2012) Andreas W. Götz et al. Journal of Chemical Theory and Computation
- Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
- (2012) Michael M. Mysinger et al. JOURNAL OF MEDICINAL CHEMISTRY
- Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
- (2012) P. J. Ballester et al. Journal of the Royal Society Interface
- Comparison of Different Approaches to Define the Applicability Domain of QSAR Models
- (2012) Faizan Sahigara et al. MOLECULES
- 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
- DEKOIS: Demanding Evaluation Kits for Objectivein SilicoScreening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions
- (2011) Simon M. Vogel et al. Journal of Chemical Information and Modeling
- Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions
- (2011) Pedro J. Ballester et al. Journal of Chemical Information and Modeling
- NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function
- (2011) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Open Babel: An open chemical toolbox
- (2011) Noel M O'Boyle et al. Journal of Cheminformatics
- A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
- (2010) Pedro J. Ballester et al. BIOINFORMATICS
- NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes
- (2010) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Exploring the Binding Site of C-Terminal Hsp90 Inhibitors
- (2010) Miriam Sgobba et al. Journal of Chemical Information and Modeling
- Extended-Connectivity Fingerprints
- (2010) David Rogers et al. Journal of Chemical Information and Modeling
- New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays
- (2010) Jonathan B. Baell et al. JOURNAL OF MEDICINAL CHEMISTRY
- Efficient Drug Lead Discovery and Optimization
- (2009) William L. Jorgensen ACCOUNTS OF CHEMICAL RESEARCH
- Enhanced HTS Hit Selection via a Local Hit Rate Analysis
- (2009) Bruce A. Posner et al. Journal of Chemical Information and Modeling
- Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
- (2009) Sebastian G. Rohrer et al. Journal of Chemical Information and Modeling
- Identifying and Characterizing Binding Sites and Assessing Druggability
- (2009) Thomas A. Halgren Journal of Chemical Information and Modeling
- 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
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