Related Experiment Video
Updated: Jun 2, 2026

Protein Target Prediction and Validation of Small Molecule Compound
Published on: February 23, 2024
Use of secondary structure element information in drug design: polypharmacology and conserved motifs in
1Intervet Innovation GmbH, Schwabenheim, Germany. oliver.koch@sp.intervet.com
Abstract:
The structure-based design of small-molecule inhibitors of protein-ligand and protein-protein interfaces is a key component of drug discovery. The underlying protein interactions can be regarded based on structural similarity of the secondary structure elements: similarities around the binding site ('ligand-sensing cores') or in the protein interface ('interface-sensing surfaces') in otherwise unrelated proteins can be useful in predicting polypharmacology and identifying new lead structures. Even small conserved motifs can provide similar interaction patterns in proteins with a completely different fold and function. The identification of these structural similarities can help in the design of new drugs by guiding further optimization. Here, the concepts and ideas based on secondary structure element similarities and their successful applications in drug design are reviewed and discussed.
More Related Videos
08:49Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
05:08Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
Related Concept Videos
Protein-protein Interfaces
Protein-Protein Interfaces
Conserved Binding Sites
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 analyses the...
Conserved Binding Sites
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 analyses the...
Structure-Activity Relationships and Drug Design
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...
Ligand Binding Sites
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...