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Benchmarking reverse docking through AlphaFold2 human proteome

https://doi.org/10.1002/pro.5167
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
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Using reverse docking to identify potential targets for ginsenosides
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Dithiocarbamates and dithiocarbonates containing 6-nitrosaccharin scaffold: Synthesis, antimycobacterial activity and in silico target prediction using ensemble docking-based reverse virtual screening
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Tools for in silico target fishing
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Capter 11 Filtering in Drug Discovery
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Predicting Selectivity and Druggability in Drug Discovery
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PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms
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Comparative Assessment of Scoring Functions: The CASF-2016 Update
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Boosting Protein–Ligand Binding Pose Prediction and Virtual Screening Based on Residue–Atom Distance Likelihood Potential and Graph Transformer
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Drug Discovery Targeting Bromodomain-Containing Protein 4
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Multitarget Approaches against Multiresistant Superbugs
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Identifying and Characterizing Binding Sites and Assessing Druggability
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
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Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
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Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities
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Large-scale prediction and testing of drug activity on side-effect targets
inferredcites →https://doi.org/10.1038/s41586-021-03819-2openalex-snapshot
Highly accurate protein structure prediction with AlphaFold
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Accurate structure prediction of biomolecular interactions with AlphaFold 3
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Protein structure alignment beyond spatial proximity
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On the origins of drug polypharmacology
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The G protein-coupled receptor repertoires of human and mouse
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Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances
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A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function
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How significant is a protein structure similarity with TM-score = 0.5?
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PDB-wide collection of binding data: current status of the PDBbind database
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CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction
inferredcites →https://doi.org/10.1093/jn/130.4.711openalex-snapshot
Uncoupling Protein Homologs: Emerging Views of Physiological Function
inferredcites →https://doi.org/10.1093/nar/gkab1061openalex-snapshot
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
inferredcites →https://doi.org/10.1093/nar/gkad751openalex-snapshot
TTD: Therapeutic Target Database describing target druggability information
inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1093/nar/gky1134openalex-snapshot
SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database
inferredcites →https://doi.org/10.1097/00041327-200020040-00001openalex-snapshot
Acute Effects of Sildenafil (Viagra) on Blue-on-Yellow and White-on-White Humphrey Perimetry
inferredcites →https://doi.org/10.1101/2021.12.20.473431openalex-snapshot
fastMSA: Accelerating Multiple Sequence Alignment with Dense Retrieval on Protein Language
inferredcites →https://doi.org/10.1110/ps.062238406openalex-snapshot
Peptide deformylase is a potential target for anti‐Helicobacter pylori drugs: Reverse docking, enzymatic assay, and X‐ray crystallography validation
inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00483.xopenalex-snapshot
New Method for Fast and Accurate Binding‐site Identification and Analysis
inferredcites →https://doi.org/10.1126/science.adn6354openalex-snapshot
AlphaFold2 structures guide prospective ligand discovery
inferredcites →https://doi.org/10.1186/1471-2105-10-1openalex-snapshot
Regularized gene selection in cancer microarray meta-analysis
inferredcites →https://doi.org/10.1186/1758-2946-6-33openalex-snapshot
In Silicotarget fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion
inferredcites →https://doi.org/10.1242/jcs.00247openalex-snapshot
The nuclear receptor superfamily
inferredcites →https://doi.org/10.1371/journal.pone.0171433openalex-snapshot
The scoring bias in reverse docking and the score normalization strategy to improve success rate of target fishing
inferredcites →https://doi.org/10.1371/journal.pone.0226484openalex-snapshot
Drug-target interaction prediction using Multi Graph Regularized Nuclear Norm Minimization
inferredcites →https://doi.org/10.1517/14728220902751632openalex-snapshot
Macrophage metalloelastase (MMP-12) as a target for inflammatory respiratory diseases
inferredcites →https://doi.org/10.1517/14740330902931524openalex-snapshot
Serotonergic drugs and valvular heart disease
inferredcites →https://doi.org/10.20900/pf20190005openalex-snapshot
Generation of a Small Library of Natural Products Designed to Cover Chemical Space Inexpensively
inferredcites →https://doi.org/10.2174/157018011794578204openalex-snapshot
Prediction of Specificity and Cross-Reactivity of Kinase Inhibitors
inferredcites →https://doi.org/10.3389/fchem.2016.00015openalex-snapshot
How Reliable Are Ligand-Centric Methods for Target Fishing?
inferredcites →https://doi.org/10.3390/ijms24032740openalex-snapshot
Exploring AlphaFold2′s Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein
inferredcites →https://doi.org/10.3390/molecules26175124openalex-snapshot
Recent Advances in In Silico Target Fishing
inferredcites →https://doi.org/10.7566/jpsj.91.064804openalex-snapshot
AlphaFold-predicted Protein Structure vs Experimentally Obtained Protein Structure: An Emphasis on the Side Chains

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Discovery, design, and engineering of enzymes based on molecular retrobiosynthesis
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AutoRevDock : An open‐source toolkit for scalable reverse docking
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Using AlphaFold and Symmetrical Docking to Predict Protein–Protein Interactions for Exploring Potential Crystallization Conditions
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Improving AlphaFold2 Performance in Virtual Screens Targeting GPCRs by Enhancing Binding-Site Conformational Sampling
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zERExtractor: An Automated Platform for Enzyme-Catalyzed Reaction Data Extraction from Scientific Literature
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Protein language models are performant in structure-free virtual screening
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OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling
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APPLICATION OF REVERSE MOLECULAR DOCKING FOR THE IDENTIFICATION OF PROTEIN TARGETS OF S-ETHYLTHIOSULFANYLATE INVOLVED IN BIOSURFACTANT BIOSYNTHESIS
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From Traditional Efficacy to Drug Design: A Review of Astragali Radix
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