ArticlePLoS computational biology2018
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Edge-aware GAT-based protein binding sites prediction.PLoS computational biology · 2026Article
- Contact-Network Phenotyping of the CDK Family Reveals Selective Distal C-Lobe Contact Redistribution by Modern CDK5 Inhibitors and a Quantitative Selectivity Landscape against CDK2 and CDK1.Journal of chemical information and modeling · 2026Article
- Spacio-Linear Screening for Ligand-Docking Cavities in Protein Structures: SLAM Algorithm.Life (Basel, Switzerland) · 2026Article
- Computer-Aided Discovery of Drugs Against Chagas Disease.Methods in molecular biology (Clifton, N.J.) · 2026Article
- OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders.PLoS computational biology · 2025Article
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- ProteinsPlus: a publicly available resource for protein structure mining.Nucleic acids research · 2025Article
- Towards a comprehensive view of the pocketome universe-biological implications and algorithmic challenges.PLoS computational biology · 2025Article
- TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.Nature communications · 2025Article
- Comprehensive detection and characterization of human druggable pockets through binding site descriptors.Nature communications · 2024Article
- Structure-Based Drug Design of ADRA2A Antagonists Derived from Yohimbine.Journal of medicinal chemistry · 2024Article
- VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites.Scientific reports · 2024Article
- Integrated Molecular Modeling and Machine Learning for Drug Design.Journal of chemical theory and computation · 2023Review
- An Intriguing Purview on the Design of Macrocyclic Inhibitors for Unexplored Protein Kinases through Their Binding Site Comparison.Pharmaceuticals (Basel, Switzerland) · 2023Review
- PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity.Journal of cheminformatics · 2023Article
- TWN-RENCOD: A novel method for protein binding site comparison.Computational and structural biotechnology journal · 2023Article
- PDBspheres: a method for finding 3D similarities in local regions in proteins.NAR genomics and bioinformatics · 2022Article
- Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.Journal of chemical information and modeling · 2022Article
- Estimating the Similarity between Protein Pockets.International journal of molecular sciences · 2022Review
- New Drug Design Avenues Targeting Alzheimer's Disease by Pharmacoinformatics-Aided Tools.Pharmaceutics · 2022Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The automated comparison of protein-ligand binding sites provides useful insights into yet unexplored site similarities. Various stages of computational and chemical biology research can benefit from this knowledge. The search for putative off-targets and the establishment of polypharmacological effects by comparing binding sites led to promising results for numerous projects. Although many cavity comparison methods are available, a comprehensive analysis to guide the choice of a tool for a specific application is wanting. Moreover, the broad variety of binding site modeling approaches, comparison algorithms, and scoring metrics impedes this choice. Herein, we aim to elucidate strengths and weaknesses of binding site comparison methodologies. A detailed benchmark study is the only possibility to rationalize the selection of appropriate tools for different scenarios. Specific evaluation data sets were developed to shed light on multiple aspects of binding site comparison. An assembly of all applied benchmark sets (ProSPECCTs-Protein Site Pairs for the Evaluation of Cavity Comparison Tools) is made available for the evaluation and optimization of further and still emerging methods. The results indicate the importance of such analyses to facilitate the choice of a methodology that complies with the requirements of a specific scientific challenge.
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Registered trials
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