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sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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The Protein Data Bank: unifying the archive
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Databases in Protein Crystallography
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Evolutionary and geometric signatures reveal ligand-binding sites across proteomes
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PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms
inferred← citeshttps://doi.org/10.1107/s0021889809048626openalex-snapshot
MLDB: macromolecule ligand database
inferred← citeshttps://doi.org/10.1109/bibm66473.2025.11356840openalex-snapshot
Beyond Exact Matches: Near-Hit Scoring for Protein Binding Site Prediction with Protein Language Models
inferred← citeshttps://doi.org/10.1109/icbcb69424.2026.11621201openalex-snapshot
REAFPocket: A Protein Pocket Prediction Method Based on Sequence-aware Voxel Representation and Dual-Channel Attention Feature Enhancement
inferred← citeshttps://doi.org/10.1109/iscon57294.2023.10112034openalex-snapshot
DeepLBS: A deep Convolutional Neural Network-Based Ligand-Binding Site Prediction Tool
inferred← citeshttps://doi.org/10.1109/tcbb.2023.3239983openalex-snapshot
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network
inferred← citeshttps://doi.org/10.1111/cbdd.12109openalex-snapshot
Sulfated Small Molecules Targeting EBV in B urkitt Lymphoma: From In Silico Screening to the Evidence of In Vitro Effect on Viral Episomal DNA
inferred← citeshttps://doi.org/10.1142/s0219720021500062openalex-snapshot
3D U-Net: A voxel-based method in binding site prediction of protein structure
inferred← citeshttps://doi.org/10.1142/s1793005710001608openalex-snapshot
UPDATING BINDING MOAD — DATA MANAGEMENT AND INFORMATION WORKFLOW
inferred← citeshttps://doi.org/10.1159/000157624openalex-snapshot
Druggable Targets and Targeted Drugs: Enhancing the Development of New Therapeutics
inferred← citeshttps://doi.org/10.11606/d.75.2025.tde-07072025-110805openalex-snapshot
Análise da seletividade de inibidores dipeptidil nitrilas: validando a especificidade por cisteíno proteases
inferred← citeshttps://doi.org/10.1186/1471-2105-12-s1-s35openalex-snapshot
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
inferred← citeshttps://doi.org/10.1186/1471-2105-8-310openalex-snapshot
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
inferred← citeshttps://doi.org/10.1186/1471-2105-9-s4-s5openalex-snapshot
AMMO-Prot: amine system project 3D-model finder
inferred← citeshttps://doi.org/10.1186/1471-2164-16-s13-s2openalex-snapshot
Computer analysis of protein functional sites projection on exon structure of genes in Metazoa
inferred← citeshttps://doi.org/10.1186/1475-2875-5-110openalex-snapshot
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
inferred← citeshttps://doi.org/10.1186/1758-2946-2-s1-p11openalex-snapshot
Where are the boundaries? Automated pocket detection for druggability studies
inferred← citeshttps://doi.org/10.1186/1758-2946-6-12openalex-snapshot
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
inferred← citeshttps://doi.org/10.1186/gb-2007-8-8-r176openalex-snapshot
Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery
inferred← citeshttps://doi.org/10.1186/s12859-020-03664-6openalex-snapshot
Predicting DNA binding protein-drug interactions based on network similarity
inferred← citeshttps://doi.org/10.1186/s13321-016-0180-0openalex-snapshot
Mapping the 3D structures of small molecule binding sites
inferred← citeshttps://doi.org/10.1186/s13321-020-00464-1openalex-snapshot
Predicting target profiles with confidence as a service using docking scores
inferred← citeshttps://doi.org/10.1186/s13321-024-00923-zopenalex-snapshot
Comparative evaluation of methods for the prediction of protein–ligand binding sites
inferred← citeshttps://doi.org/10.1186/s40360-017-0128-7openalex-snapshot
Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects
inferred← citeshttps://doi.org/10.1207/s15327647jcd0703_5openalex-snapshot
The Development of Learning
inferred← citeshttps://doi.org/10.1248/bpb.b21-00324openalex-snapshot
Application of Reverse Docking in the Research of Small Molecule Drugs and Traditional Chinese Medicine
inferred← citeshttps://doi.org/10.1371/annotation/95078306-dc3b-4441-b2b1-dd986b734570openalex-snapshot
Correction: Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002326openalex-snapshot
Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005293openalex-snapshot
Normal Modes Expose Active Sites in Enzymes
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006483openalex-snapshot
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)
inferred← citeshttps://doi.org/10.1371/journal.pone.0012214openalex-snapshot
Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
inferred← citeshttps://doi.org/10.1371/journal.pone.0050240openalex-snapshot
Identification of Nucleotide-Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity
inferred← citeshttps://doi.org/10.1371/journal.pone.0065894openalex-snapshot
Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key
inferred← citeshttps://doi.org/10.1371/journal.pone.0135246openalex-snapshot
In Silico Adoption of an Orphan Nuclear Receptor NR4A1
inferred← citeshttps://doi.org/10.1371/journal.pone.0223596openalex-snapshot
CavBench: A benchmark for protein cavity detection methods
inferred← citeshttps://doi.org/10.1517/17460441.3.4.391openalex-snapshot
A structural biology view of target drugability
inferred← citeshttps://doi.org/10.18632/oncotarget.3789openalex-snapshot
CEMTDD: The database for elucidating the relationships among herbs, compounds, targets and related diseases for Chinese ethnic minority traditional drugs
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3687338/v1openalex-snapshot
Protein structure-based organic chemistry-driven ligand design from ultra-large chemical spaces
inferred← citeshttps://doi.org/10.2174/138620711795767811openalex-snapshot
Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction
inferred← citeshttps://doi.org/10.2174/1568026619666190816101948openalex-snapshot
Virtual Screening Techniques in Drug Discovery: Review and Recent Applications
inferred← citeshttps://doi.org/10.3389/fbioe.2022.822392openalex-snapshot
Prediction of DNA-Binding Protein–Drug-Binding Sites Using Residue Interaction Networks and Sequence Feature
inferred← citeshttps://doi.org/10.3389/fchem.2023.1089714openalex-snapshot
Mining the Protein Data Bank to inspire fragment library design
inferred← citeshttps://doi.org/10.3389/fonc.2023.1061595openalex-snapshot
Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions
inferred← citeshttps://doi.org/10.3389/fphar.2021.689767openalex-snapshot
Maprotiline Suppresses Cholesterol Biosynthesis and Hepatocellular Carcinoma Progression Through Direct Targeting of CRABP1
inferred← citeshttps://doi.org/10.3389/fphar.2022.874637openalex-snapshot
Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Vitamin D3 and COVID-19 as Potential Therapeutic Targets
inferred← citeshttps://doi.org/10.3390/ijms12064027openalex-snapshot
Systematic Approaches towards the Development of Host-Directed Antiviral Therapeutics
inferred← citeshttps://doi.org/10.3390/ijms20184331openalex-snapshot
Molecular Docking: Shifting Paradigms in Drug Discovery
inferred← citeshttps://doi.org/10.3390/ijms21062243openalex-snapshot
Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB)
inferred← citeshttps://doi.org/10.3390/ijms21145152openalex-snapshot
A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0
inferred← citeshttps://doi.org/10.3390/ijms22136830openalex-snapshot
‘All That Glitters Is Not Gold’: High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses
inferred← citeshttps://doi.org/10.3390/molecules21111554openalex-snapshot
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors
inferred← citeshttps://doi.org/10.3390/molecules25122840openalex-snapshot
Costunolide Plays an Anti-Neuroinflammation Role in Lipopolysaccharide-Induced BV2 Microglial Activation by Targeting Cyclin-Dependent Kinase 2
inferred← citeshttps://doi.org/10.3410/f.736506713.793564542openalex-snapshot
Faculty Opinions recommendation of Updates to binding MOAD (mother of all databases): polypharmacology tools and their utility in drug repurposing.
inferred← citeshttps://doi.org/10.4155/fmc.12.147openalex-snapshot
Chemogenomics In Drug Discovery: Computational Methods Based On The Comparison Of Binding Sites
inferred← citeshttps://doi.org/10.4155/fmc.13.207openalex-snapshot
Reverse Docking: A Powerful Tool for Drug Repositioning and Drug Rescue
inferred← citeshttps://doi.org/10.53879/id.58.08.12930openalex-snapshot
COMPUTATIONAL APPROACHES FOR DRUG DISCOVERY FROM MEDICINAL PLANTS IN THE ERA OF DATA DRIVEN RESEARCH
inferred← citeshttps://doi.org/10.5772/intechopen.100109openalex-snapshot
Using the Structural Kinome to Systematize Kinase Drug Discovery
inferred← citeshttps://doi.org/10.6084/m9.figshare.12680586openalex-snapshot
Additional file 1 of Predicting DNA binding protein-drug interactions based on network similarity
inferred← citeshttps://doi.org/10.6084/m9.figshare.13101273openalex-snapshot
Additional file 1 of Predicting target profiles with confidence as a service using docking scores
inferred← citeshttps://doi.org/10.64898/2026.01.28.702257openalex-snapshot
Seq2Pocket: Augmenting protein language models for spatially consistent binding site prediction
inferred← citeshttps://doi.org/10.70675/00fff70azab21z46edz8364z60031c95c00fopenalex-snapshot
Applications of proteochemometrics (PCM) : from species extrapolation to cell-line sensitivity modelling
inferred← citeshttps://doi.org/10.70675/b169d9faz00f4z43e4z8502z99fe6aa98948openalex-snapshot
Développement d'une plateforme informatique hétérogène appliquée à la pharmacognosie
inferred← citeshttps://doi.org/10.70675/ff9e5fd3za154z4b07zb082z0544574f7124openalex-snapshot
Rational design of bioactive molecules for antibiotic purposes
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