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

Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

17.9K
17.9K
Network Covalent Solids02:18

Network Covalent Solids

13.6K
Network covalent solids contain a three-dimensional network of covalently bonded atoms as found in the crystal structures of nonmetals like diamond, graphite, silicon, and some covalent compounds, such as silicon dioxide (sand) and silicon carbide (carborundum, the abrasive on sandpaper). Many minerals have networks of covalent bonds.
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
13.6K
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
Van der Waals Interactions01:24

Van der Waals Interactions

64.3K
Atoms and molecules interact with each other through intermolecular forces. These electrostatic forces arise from attractive or repulsive interactions between particles with permanent, partial, or temporary charges. The intermolecular forces between neutral atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively known as van der Waals forces.
64.3K
Molecular Models02:00

Molecular Models

39.1K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
39.1K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

13.2K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
13.2K

You might also read

Related Articles

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

Sort by
Same author

Rediscovering Diazaborines: Synthesis and Bioactivity Profiling of Boron-Containing FabI Inhibitors against Gram-Negative Bacteria.

Journal of medicinal chemistry·2026
Same author

EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment.

Nucleic acids research·2025
Same author

Expanding the Paradigm of Structure-Based Drug Design: Molecular Dynamics Simulations Support the Development of New Pyridine-Based Protein Kinase C-Targeted Agonists.

Journal of medicinal chemistry·2023
Same author

Analysis of Biologics Molecular Descriptors towards Predictive Modelling for Protein Drug Development Using Time-Gated Raman Spectroscopy.

Pharmaceutics·2022
Same author

Exploration of Pyrazolo[1,5-a]pyrimidines as Membrane-Bound Pyrophosphatase Inhibitors.

ChemMedChem·2021
Same author

Binding Site Interactions of Modulators of Breast Cancer Resistance Protein, Multidrug Resistance-Associated Protein 2, and P-Glycoprotein Activity.

Molecular pharmaceutics·2020
Same journal

SpaceExpander: An Automated System for Drafting Markush Claims to Expand Chemical Space.

Molecular informatics·2026
Same journal

A Structure-Informed Atlas of Venom-Derived Peptides Reveals the Organization of Chemical Space.

Molecular informatics·2026
Same journal

ConGen: Targeted Molecule Generation Through Contrastive Learning and Latent Optimization.

Molecular informatics·2026
Same journal

Novel Molecules Generation Using Graph Generative Adversarial Networks.

Molecular informatics·2026
Same journal

An Attention-Driven Graph Transformer With Nonlinear Modeling and Neuro-Fuzzy Fusion for High-Order Toxic Molecular Graph Learning.

Molecular informatics·2026
Same journal

Molecular Modeling and Chemoinformatics in Ukraine.

Molecular informatics·2026
See all related articles

Related Experiment Video

Updated: Aug 14, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.9K

Exploring cooperative molecular contacts using a PostgreSQL database system.

Mael A Briand1, Loïc Dreano1, Ashenafi Legehar1

  • 1Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland.

Molecular Informatics
|January 18, 2023
PubMed
Summary
This summary is machine-generated.

We developed a database to analyze protein molecular contacts, finding that nearby carboxylate atoms shorten Ser-OH..N-His bonds in catalytic triads. This tool helps identify potential functions in unannotated proteins.

Keywords:
catalytic triaddatabaseprotein structure

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

5.1K
Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
11:21

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Published on: January 20, 2022

3.5K

Related Experiment Videos

Last Updated: Aug 14, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.9K
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

5.1K
Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
11:21

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Published on: January 20, 2022

3.5K

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biochemistry

Background:

  • Cooperative molecular contacts are crucial for protein structure and function, particularly in ligand binding.
  • Understanding these interactions requires efficient methods for analyzing atomic environments and relationships within proteins.

Purpose of the Study:

  • To create a flexible PostgreSQL database for mining molecular contacts based on atomic environments.
  • To investigate the role of carboxylate groups in the Ser-His-Asp/Glu catalytic triad and identify potential catalytic functions in unannotated proteins.

Main Methods:

  • Construction of a PostgreSQL database storing protein structural information as atomic environments.
  • Flexible querying of the database to mine molecular contacts, focusing on catalytic triads (Ser-His-Asp/Glu).
  • Inclusion of ligand atoms (using Sybyl atom types) for analyzing interactions, exemplified by evaluating counter-ion proportions for ligand carboxylates.

Main Results:

  • The presence of carboxylate oxygen atoms near histidine residues was associated with shorter Ser-OH..N-His hydrogen bonds in the PDB30 dataset.
  • Prospective mining of catalytic triads in unannotated proteins suggested potential catalytic functions for these proteins.
  • The database system successfully incorporated ligand atom information, enabling analysis of ligand-protein interactions like counter-ion binding.

Conclusions:

  • The developed database provides a powerful tool for flexible mining of molecular contacts and protein structural analysis.
  • The findings highlight the influence of carboxylate proximity on catalytic triad geometry and suggest a method for functional annotation of proteins.
  • The system's ability to include ligand atoms broadens its applicability to studying drug-target interactions and other ligand-mediated processes.