ArticleComputational and structural biotechnology journal2014
Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison.
Article in Computational and structural biotechnology journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- GRADE and X-GRADE: Unveiling Novel Protein-Ligand Interaction Fingerprints Based on GRAIL Scores.Journal of chemical information and modeling · 2025Article
- Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery.Biomolecules · 2024Review
- Improving structure-based protein-ligand affinity prediction by graph representation learning and ensemble learning.PloS one · 2024Article
- An overview of recent advances and challenges in predicting compound-protein interaction (CPI).Medical review (2021) · 2023Review
- A practical guide to machine-learning scoring for structure-based virtual screening.Nature protocols · 2023Review
- Ligand-based virtual screening, molecular docking, and molecular dynamics of eugenol analogs as potential acetylcholinesterase inhibitors with biological activity against Spodoptera frugiperda.Molecular diversity · 2022Article
- Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.Frontiers in bioinformatics · 2022Article
- Deep Learning in Virtual Screening: Recent Applications and Developments.International journal of molecular sciences · 2021Review
- A review on compound-protein interaction prediction methods: Data, format, representation and model.Computational and structural biotechnology journal · 2021Review
- graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein-Ligand Complexes.ACS omega · 2020Article
- Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.Bioinformatics (Oxford, England) · 2019Article
- Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.Journal of chemical information and modeling · 2016Article
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4 authors.
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Abstract
We describe SILIRID (Simple Ligand-Receptor Interaction Descriptor), a novel fixed size descriptor characterizing protein-ligand interactions. SILIRID can be obtained from the binary interaction fingerprints (IFPs) by summing up the bits corresponding to identical amino acids. This results in a vector of 168 integer numbers corresponding to the product of the number of entries (20 amino acids and one cofactor) and 8 interaction types per amino acid (hydrophobic, aromatic face to face, aromatic edge to face, H-bond donated by the protein, H-bond donated by the ligand, ionic bond with protein cation and protein anion, and interaction with metal ion). Efficiency of SILIRID to distinguish different protein binding sites has been examined in similarity search in sc-PDB database, a druggable portion of the Protein Data Bank, using various protein-ligand complexes as queries. The performance of retrieval of structurally and evolutionary related classes of proteins was comparable to that of state-of-the-art approaches (ROC AUC ≈ 0.91). SILIRID can efficiently be used to visualize chemogenomic space covered by sc-PDB using Generative Topographic Mapping (GTM): sc-PDB SILIRID data form clusters corresponding to different protein types.
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