ArticleNucleic acids research2015
sc-PDB: a 3D-database of ligandable binding sites--10 years on.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed.
- EmmaEmb: A quantitative framework for analyzing embedding spaces in molecular biology.Patterns (New York, N.Y.) · 2026Article
- DSC-bsite: a dynamic-static collaborative multimodal graph learning method for protein-small molecule binding site prediction.Molecular diversity · 2026Article
- Panax quinquefolium saponin decreases atherosclerosis in ovariectomized ApoEChinese medicine · 2026Article
- Synthesis and in vitro/in silico evaluation studies of arensulfonylhydrazinoxamoyl amine and amino acid derivatives as preliminary acetylcholinesterase inhibitors.Scientific reports · 2026Article
- Sequence-based drug-target binding site pre-training enables cryptic pocket detection and improves binding affinity and kinetics prediction.Journal of cheminformatics · 2026Article
- Sequence-based Drug-Target Binding Site Pretraining Enables Cryptic Pocket Detection and Improves Binding Affinity and Kinetics Prediction.bioRxiv : the preprint server for biology · 2026Article
- LiBRe: A Ligand-Aware Sequence-Based Binding Residue Prediction Model for Virtual Screening.Journal of chemical information and modeling · 2026Article
- SwinSite: 3D Structure-Based Prediction of Protein-Ligand Binding Sites Using a Combined Vision Transformer and Convolution Model.Journal of chemical information and modeling · 2026Article
- Accurate Identification of Protein Binding Sites for All Drug Modalities Using ALLSites.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures.Computational and structural biotechnology journal · 2026Article
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- A Systematic Review of Drug-Related InteractionsUtilizing Deep Learning and LLMs for Prediction and Mitigation.ACS omega · 2025Review
- VN-EGNN: E(3)- and SE(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification.Journal of cheminformatics · 2025Article
- Incorporating targeted protein structure in deep learning methods for molecule generation in computational drug design.Chemical science · 2025Review
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
- A structure-oriented kinetics dataset of enzyme-substrate interactions.Scientific data · 2025Article
- Benchmarking 3D Structure-Based Molecule Generators.Journal of chemical information and modeling · 2025Article
- Article
- Eno1 in sepsis-induced coagulopathy: a pleiotropic mechanism hypothesis involving immunomodulation and endothelial dysfunction.Thrombosis journal · 2025Article
52 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The sc-PDB database (available at http://bioinfo-pharma.u-strasbg.fr/scPDB/) is a comprehensive and up-to-date selection of ligandable binding sites of the Protein Data Bank. Sites are defined from complexes between a protein and a pharmacological ligand. The database provides the all-atom description of the protein, its ligand, their binding site and their binding mode. Currently, the sc-PDB archive registers 9283 binding sites from 3678 unique proteins and 5608 unique ligands. The sc-PDB database was publicly launched in 2004 with the aim of providing structure files suitable for computational approaches to drug design, such as docking. During the last 10 years we have improved and standardized the processes for (i) identifying binding sites, (ii) correcting structures, (iii) annotating protein function and ligand properties and (iv) characterizing their binding mode. This paper presents the latest enhancements in the database, specifically pertaining to the representation of molecular interaction and to the similarity between ligand/protein binding patterns. The new website puts emphasis in pictorial analysis of data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.