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PrePCI : A structure‐ and chemical similarity‐informed database of predicted protein compound interactions

https://doi.org/10.1002/pro.4594
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1 of the 84 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-11): 10.7554/elife.12248 (notice 2018-04-12).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Sensitivity of TP53‐Mutated Cancer Cells to the Phytoestrogen Genistein Is Associated With Direct Inhibition of Plk1 Activity
inferredcites →https://doi.org/10.1002/pro.4594openalex-snapshot
PrePCI : A structure‐ and chemical similarity‐informed database of predicted protein compound interactions
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Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
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Approaches to Measure Chemical Similarity – a Review
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Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins
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Similarity Searching Using 2D Structural Fingerprints
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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
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Advances in experimental medicine and biology
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ACOT4 accumulation via AKT-mediated phosphorylation promotes pancreatic tumourigenesis
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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ
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Specificity and Commonality of the Phosphoinositide-Binding Proteome Analyzed by Quantitative Mass Spectrometry
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Binding Affinity Prediction by Pairwise Function Based on Neural Network
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General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps
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Protein–Ligand Scoring with Convolutional Neural Networks
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FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules
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Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein–Ligand Binding
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WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand–Receptor Docking
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SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
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Extended-Connectivity Fingerprints
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Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets
inferredcites →https://doi.org/10.1021/ci500319fopenalex-snapshot
Structural Protein?Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study
inferredcites →https://doi.org/10.1021/ci900043ropenalex-snapshot
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
inferredcites →https://doi.org/10.1021/jm8009958openalex-snapshot
Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
inferredcites →https://doi.org/10.1038/cddis.2013.308openalex-snapshot
WWOX suppresses autophagy for inducing apoptosis in methotrexate-treated human squamous cell carcinoma
inferredcites →https://doi.org/10.1038/nbt.2999openalex-snapshot
Global analysis of protein structural changes in complex proteomes
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Relating protein pharmacology by ligand chemistry
inferredcites →https://doi.org/10.1038/ncomms3701openalex-snapshot
Highly confined ions store charge more efficiently in supercapacitors
inferredcites →https://doi.org/10.1038/nmeth.1818openalex-snapshot
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
inferredcites →https://doi.org/10.1038/s41418-018-0095-6openalex-snapshot
Epigenetic restriction of Hippo signaling by MORC2 underlies stemness of hepatocellular carcinoma cells
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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells
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Systematic identification of metabolites controlling gene expression in E. coli
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PHD1 controls muscle mTORC1 in a hydroxylation-independent manner by stabilizing leucyl tRNA synthetase
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inferredcites →https://doi.org/10.1038/srep46710openalex-snapshot
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inferredcites →https://doi.org/10.1080/14789450.2021.1962302openalex-snapshot
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inferredcites →https://doi.org/10.1093/bib/bbac353openalex-snapshot
Multiple similarity drug–target interaction prediction with random walks and matrix factorization
inferredcites →https://doi.org/10.1093/bioinformatics/btn162openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/btq112openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/bty374openalex-snapshot
Development and evaluation of a deep learning model for protein–ligand binding affinity prediction
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gkaa971openalex-snapshot
PubChem in 2021: new data content and improved web interfaces
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/gkac1052openalex-snapshot
UniProt: the Universal Protein Knowledgebase in 2023
inferredcites →https://doi.org/10.1093/nar/gkq1189openalex-snapshot
CDD: a Conserved Domain Database for the functional annotation of proteins
inferredcites →https://doi.org/10.1093/nar/gks1258openalex-snapshot
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
inferredcites →https://doi.org/10.1093/nar/gky1033openalex-snapshot
PubChem 2019 update: improved access to chemical data
inferredcites →https://doi.org/10.1093/nar/gky1114openalex-snapshot
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inferredcites →https://doi.org/10.1182/bloodadvances.2017005173openalex-snapshot
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inferredcites →https://doi.org/10.1186/1758-2946-3-1openalex-snapshot
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inferredcites →https://doi.org/10.1186/s13321-014-0049-zopenalex-snapshot
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inferredcites →https://doi.org/10.1186/s13321-015-0069-3openalex-snapshot
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inferredcites →https://doi.org/10.12688/f1000research.2-199.v1openalex-snapshot
Advancing the activity cliff concept
inferredcites →https://doi.org/10.1371/journal.pcbi.1004760openalex-snapshot
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction
inferredcites →https://doi.org/10.1371/journal.pcbi.1005135openalex-snapshot
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
inferredcites →https://doi.org/10.1371/journal.pcbi.1006619openalex-snapshot
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inferredcites →https://doi.org/10.15252/embr.202050218openalex-snapshot
Paladin is a phosphoinositide phosphatase regulating endosomal VEGFR2 signalling and angiogenesis
inferredcites →https://doi.org/10.15252/msb.20188503openalex-snapshot
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
inferredcites →https://doi.org/10.15252/msb.20199008openalex-snapshot
Systematic mapping of protein‐metabolite interactions in central metabolism of Escherichia coli
inferredcites →https://doi.org/10.3390/biom10060862openalex-snapshot
The Regulatory Role of Key Metabolites in the Control of Cell Signaling
inferredcites →https://doi.org/10.3390/biom10101453openalex-snapshot
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inferredcites →https://doi.org/10.3390/ijms21218342openalex-snapshot
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inferredcites →https://doi.org/10.48550/arxiv.1510.02855openalex-snapshot
AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery
inferredcites →https://doi.org/10.7554/elife.12248openalex-snapshot
RETRACTED: A mathematical model explains saturating axon guidance responses to molecular gradients
inferredcites →https://doi.org/10.7554/elife.18715openalex-snapshot
A computational interactome and functional annotation for the human proteome

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9783527840748.ch10openalex-snapshot
AI ‐Based Protein Structure Predictions and Their Implications in Drug Discovery
inferred← citeshttps://doi.org/10.1002/pro.5027openalex-snapshot
MAGPIE: An interactive tool for visualizing and analyzing protein–ligand interactions
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00076-2openalex-snapshot
A Review of Protein-Protein Interaction Databases
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2026.108803openalex-snapshot
Decoding polyphenol–protein interactions with deep learning: From molecular mechanisms to food applications
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.03.015openalex-snapshot
Databases of ligand-binding pockets and protein-ligand interactions
inferred← citeshttps://doi.org/10.1016/j.jmb.2023.168052openalex-snapshot
PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c01885openalex-snapshot
In Silico Tools to Score and Predict Cholesterol–Protein Interactions
inferred← citeshttps://doi.org/10.1073/pnas.2220778120openalex-snapshot
Contrastive learning in protein language space predicts interactions between drugs and protein targets
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag290openalex-snapshot
HKD-CPI: high-order knowledge distillation enhanced inductive compound-protein interaction prediction
inferred← citeshttps://doi.org/10.1101/2022.12.06.519374openalex-snapshot
Learning the Drug-Target Interaction Lexicon
inferred← citeshttps://doi.org/10.1101/2023.10.08.561457openalex-snapshot
Compound Mechanism of Action and Polypharmacology can be Elucidated by Large-Scale Perturbational Profile Analysis
inferred← citeshttps://doi.org/10.1109/imcom64595.2025.10857588openalex-snapshot
MuFAl: A Universal Drug-Target Interaction Prediction Framework
inferred← citeshttps://doi.org/10.1186/s13321-025-01125-xopenalex-snapshot
The Human Omnibus of Targetable Pockets
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3578471/v1openalex-snapshot
In silico Screening of Plectranthus ampoinicus and Hyptis suaveolens Phytochemicals: Novel Repellents Targeting Odorant Binding Proteins of Aedes aegypti and Aedes albopictus
inferred← citeshttps://doi.org/10.2174/0122113525306071240613043139openalex-snapshot
In silico Screening of Plectranthus amboinicus and Hyptis suaveolens Phytochemicals: Novel Repellents Targeting Odorant Binding Proteins of Aedes aegypti and Aedes albopictus
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