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Related Concept Videos

Molecular Models02:00

Molecular Models

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.
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...
Protein-protein Interfaces02:04

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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...
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Intermolecular Forces

Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen bonds, and dispersion...
Intermolecular Forces03:13

Intermolecular Forces

Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen bonds, and dispersion...
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Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Published on: July 19, 2024

Modeling macro-molecular interfaces with Intervor.

Sébastien Loriot1, Frédéric Cazals

  • 1INRIA Sophia-Antipolis-Méditerranée, Algorithms-Biology-Structure, Sophia-Antipolis, France.

Bioinformatics (Oxford, England)
|February 9, 2010
PubMed
Summary
This summary is machine-generated.

Intervor software generates a detailed, parameter-free model of macromolecular interfaces using atomic alpha-complexes. This tool identifies direct and water-mediated contacts, defines a Voronoi interface, and analyzes atomic depth for deeper structural insights.

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Related Experiment Videos

Last Updated: Jun 16, 2026

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • Intervor software is accessible via a web server and downloadable binary.
  • Plugins for VMD and Pymol are available, enhancing its integration into existing workflows.

Purpose of the Study:

  • To introduce Intervor, a novel software for computing parameter-free representations of macromolecular interfaces.
  • To provide a detailed geometric and topological description of these interfaces.

Main Methods:

  • Utilizes the alpha-complex of atoms to represent macromolecular interfaces.
  • Identifies direct and water-mediated atomic contacts between interacting partners.
  • Defines a Voronoi interface with calculable geometric properties like surface area and curvature.

Main Results:

  • Computes a comprehensive interface model, including direct and water-mediated interactions.
  • Generates a geometric complex (Voronoi interface) with straightforward descriptions.
  • Enables the analysis of atomic depth within the interface, moving beyond core-rim distinctions.

Conclusions:

  • Intervor offers a robust method for analyzing macromolecular interfaces.
  • The software facilitates investigations into structure-property relationships, including residue conservation, polarity, and water dynamics.
  • Its features support in-depth studies of mutagenesis data and other interface-related biological phenomena.