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Related Concept Videos

Ligand Binding Sites02:40

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...
Ligand Binding Sites02:40

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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Conserved Binding Sites01:49

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 analyses the...

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Related Experiment Video

Updated: Jun 4, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Published on: July 8, 2025

ReverseScreen3D: a structure-based ligand matching method to identify protein targets.

Sarah L Kinnings1, Richard M Jackson

  • 1Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.

Journal of Chemical Information and Modeling
|March 3, 2011
PubMed
Summary
This summary is machine-generated.

We developed ReverseScreen3D, a novel reverse virtual screening (VS) method, to predict potential protein targets for compounds. This method aids in identifying drug toxicity causes and potential off-targets for existing medications.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Ligand promiscuity is a common cause of drug toxicity.
  • Predicting unintended protein targets of small molecules is crucial for drug safety.

Purpose of the Study:

  • To develop and evaluate a novel reverse virtual screening (VS) method, ReverseScreen3D, for predicting potential protein targets of query compounds.
  • To assess the performance of 2D and 3D structure-based comparisons in identifying true targets.

Main Methods:

  • Developed ReverseScreen3D, a VS method utilizing 2D fingerprint and 3D geometric matching.
  • Created a target database of known ligand bioactive conformations.
  • Evaluated performance using known multi-target small molecule inhibitors.

Main Results:

  • ReverseScreen3D significantly enriches true protein targets in screening results.
  • 3D structural comparison enhances early target enrichment compared to 2D methods alone.
  • The 3D method shows efficacy even without significant 2D similarity.

Conclusions:

  • ReverseScreen3D is an effective tool for predicting compound protein targets and potential off-targets.
  • The method can aid in understanding drug toxicity mechanisms.
  • A web server is available for public use.