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Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

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Spacio-Linear Screening for Ligand-Docking Cavities in Protein Structures: SLAM Algorithm.

Julia Panov^1,2, Alexander Elbert¹, Dean S Rosenthal³

¹Tauber Bioinformatics Research Center, University of Haifa, Haifa 3103301, Israel.

Life (Basel, Switzerland)

|February 27, 2026

Summary

This summary is machine-generated.

SLAM, a novel structural screening tool, identifies similar ligand-binding sites in proteins. This accelerates drug discovery and environmental toxicology research by finding new protein targets and predicting toxicant interactions.

Keywords:

3D screening binding site similarity protein ligand docking structural alignment

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Area of Science:

Computational Biology
Structural Bioinformatics
Drug Discovery

Background:

Identifying structurally similar ligand-binding sites aids drug repurposing and understanding protein function.
Existing structural screening tools often lack sensitivity and scalability.

Purpose of the Study:

To develop a novel algorithm for discovering novel protein targets for a ligand using a known ligand-binding query protein.
To present SLAM (Spacio-Linear Alignment of Macromolecules) for detecting local 3D similarities between protein structures.

Main Methods:

SLAM encodes spatial substructure neighborhoods into linear sequences of annotated atoms.
Pairwise sequence alignment and distance-correlation scoring identify structural matches.
Benchmarking performed using the Kahraman-36 dataset against the ProBiS algorithm.

Main Results:

SLAM outperforms ProBiS in true-positive rate for predicting ligand-docking compatibility.
Identified potential inhibitors for CRISPR-Cas proteins.
Predicted novel binding partners for toxic per- and polyfluoroalkyl substances (PFAS).

Conclusions:

SLAM is a robust, efficient, and flexible tool for structural screening.
It detects subtle physicochemical compatibilities between protein surfaces.
SLAM promises to accelerate target discovery in pharmacology and environmental toxicology.