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Related Concept Videos

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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...
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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Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...

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Related Experiment Video

Updated: May 15, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

PubChem3D: conformer ensemble accuracy.

Sunghwan Kim1, Evan E Bolton, Stephen H Bryant

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov.

Journal of Cheminformatics
|January 8, 2013
PubMed
Summary
This summary is machine-generated.

PubChem3D conformer models maintain accuracy after clustering, though some degradation occurs. Accuracy is predictable and improves with smaller, less flexible molecules.

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Last Updated: May 15, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

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08:49

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 chemistry
  • Cheminformatics
  • Structural biology

Background:

  • PubChem provides substance data and biological activity information.
  • PubChem3D offers computationally derived 3D structures for small molecules.
  • The quality of 3D conformer models is crucial for PubChem3D tools and services.

Purpose of the Study:

  • To assess the accuracy loss in PubChem3D conformer models after clustering.
  • To evaluate the impact of this accuracy loss on 3D similarity analysis.

Main Methods:

  • Generated conformer models for 47,123 experimentally determined small molecules.
  • Clustered conformers to reduce model size (max 500 per molecule).
  • Evaluated accuracy using RMSD, shape-Tanimoto (STST-opt), and color-Tanimoto (CTCT-opt) metrics.

Main Results:

  • Clustering slightly decreased conformer model accuracy.
  • Average RMSD increased by 0.18 Å; shape and color Tanimoto scores decreased.
  • Accuracy degradation was linear with molecular size and flexibility.

Conclusions:

  • PubChem3D conformer model accuracy performs as designed.
  • 3D similarity analysis accuracy degrades linearly with molecular size and flexibility.
  • Expected minimum accuracy for ensembles is predictable and improves for smaller/less flexible molecules.