Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.7K
Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Exploring natural phenolic compounds as amyloid-beta fibril inhibitors: computational insights for Alzheimer's disease.

Journal of biomolecular structure & dynamics·2026
Same author

One-pot cascade synthesis of 2-aminomaleimides and thioaminomaleimides: an alternative fluorogenic platform capable of drug conjugation.

Organic & biomolecular chemistry·2026
Same author

UV Light-Mediated Generation of Ketyl Radicals with a Concurrent 1,2-Boron Shift and One-Pot Synthesis of Benzoxaboroles under Continuous-Flow Conditions.

Organic letters·2025
Same author

Correction: SAVI Space-combinatorial encoding of the billion-size synthetically accessible virtual inventory.

Scientific data·2025
Same author

SAVI Space-combinatorial encoding of the billion-size synthetically accessible virtual inventory.

Scientific data·2025
Same author

What impact does tautomerism have on drug discovery and development?

Expert opinion on drug discovery·2024
Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026
Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026
Same journal

Derisking Affinity Optimization for Macrocycles and Cyclic Peptides: High-Precision Free Energy Simulations across Five Diverse Targets.

Journal of chemical information and modeling·2026
Same journal

An End-User Audit of Reproducibility, Data Leakage, and Overfitting of the Top-Ranked ADMET Prediction Models in TDC Leaderboards.

Journal of chemical information and modeling·2026
Same journal

PFASGroups: An Open-Source Framework for Automated Identification, Structural Classification, and Prioritization of Per- and Polyfluoroalkyl Substances.

Journal of chemical information and modeling·2026
Same journal

DeepKbhb: Context-Aware Prediction of Human Lysine β-Hydroxybutyrylation Sites.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: Jun 12, 2025

A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions
07:40

A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions

Published on: May 27, 2021

4.1K

Tautomeric Conflicts in Forty Small-Molecule Databases.

Devendra K Dhaked1, Marc C Nicklaus1

  • 1Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland 21702, United States.

Journal of Chemical Information and Modeling
|September 24, 2024
PubMed
Summary
This summary is machine-generated.

Tautomeric conflicts, where different molecular structures are incorrectly identified as the same, were found in all analyzed chemical databases. These conflicts, affecting over 210 million structures, highlight the need for improved chemical data standardization.

More Related Videos

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.0K
Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
08:15

Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease

Published on: May 10, 2024

512

Related Experiment Videos

Last Updated: Jun 12, 2025

A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions
07:40

A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions

Published on: May 27, 2021

4.1K
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.0K
Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
08:15

Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease

Published on: May 10, 2024

512

Area of Science:

  • Chemistry
  • Cheminformatics
  • Computational Chemistry

Background:

  • Chemical databases contain vast numbers of molecular structures.
  • Accurate representation of molecular structures is crucial for chemical research and drug discovery.
  • Tautomerism, the existence of molecules differing in the position of a proton and an adjacent single and double bond, can lead to structural ambiguity.

Purpose of the Study:

  • To identify and quantify tautomeric conflicts across a diverse range of chemical databases.
  • To assess the prevalence and impact of tautomeric errors in large-scale chemical data.
  • To evaluate the effectiveness of existing tautomeric transformation rules.

Main Methods:

  • Analysis of 40 chemical databases (totaling over 210 million structures).
  • Application of 119 tautomeric transformation rules (SMIRKS format) to detect conflicts.
  • Categorization of tautomerism into prototropic, ring-chain, and valence types.

Main Results:

  • All analyzed databases exhibited intra-database tautomeric conflicts.
  • 79 out of 119 tested tautomeric rules identified at least one conflict.
  • Conflict rates were typically in the low tenths of a percent, translating to over 100,000 cases in the largest databases.

Conclusions:

  • Tautomeric conflicts are a pervasive issue in chemical databases.
  • The findings underscore the necessity for robust algorithms and standardized rules for tautomer identification.
  • Improved data curation is essential for reliable chemical information retrieval and analysis.