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Related Concept Videos

Contact Angle01:13

Contact Angle

When a solid is dipped inside a liquid, the liquid surface becomes curved near the contact. For some solid–liquid interfaces, the liquid is pulled up along the solid, while for others, the liquid surface is convex or depressed near the solid surface. This phenomenon can be explained using the concept of cohesive and adhesive forces.
The adhesive force is the molecular force between molecules of different materials, that is, between the molecules of the solid and the liquid. The cohesive force...
Coordinates and Map Projections01:29

Coordinates and Map Projections

Coordinates and map projections are essential tools in accurately representing the Earth's surface for various applications, ranging from navigation to spatial analysis. The latitude and longitude coordinate system is a universally recognized framework for defining locations. Latitude specifies the distance of a point north or south of the equator, measured in degrees from 0° at the equator to 90° at the poles. Longitude indicates a location's position east or west of the prime meridian,...
Coplanar Forces01:25

Coplanar Forces

Consider an object upon which multiple forces are acting. If the lines of action of each force lie within the same plane, the system can be considered coplanar. The Cartesian vector form can be used to resolve each force into its respective components. For a coplanar system, the system will be in equilibrium if each component of the resultant force equals zero and the resultant force on the system is zero. If the sum of the forces is not equal to zero, then the object will not be in equilibrium...
Elastic Collisions: Case Study01:15

Elastic Collisions: Case Study

Elastic collision of a system demands conservation of both momentum and kinetic energy. To solve problems involving one-dimensional elastic collisions between two objects, the equations for conservation of momentum and conservation of internal kinetic energy can be used. For the two objects, the sum of momentum before the collision equals the total momentum after the collision. An elastic collision conserves internal kinetic energy, and so the sum of kinetic energies before the collision equals...
Collisions in Multiple Dimensions: Problem Solving01:06

Collisions in Multiple Dimensions: Problem Solving

In multiple dimensions, the conservation of momentum applies in each direction independently. Hence, to solve collisions in multiple dimensions, we should write down the momentum conservation in each direction separately. To help understand collisions in multiple dimensions, consider an example.
A small car of mass 1,200 kg traveling east at 60 km/h collides at an intersection with a truck of mass 3,000 kg traveling due north at 40 km/h. The two vehicles are locked together. What is the...
Contact-dependent Signaling01:19

Contact-dependent Signaling

Contact-dependent signaling, as the name suggests, requires that communicating cells be in direct contact with each other. This is achieved either through receptor-ligand interactions or by specialized cytoplasmic channels that allow the flow of small molecules between cells. In animal cells, channels called gap junctions facilitate contact-dependent signaling in certain tissues, whereas, plasmodesmata perform a similar function in plants.
Gap Junctions
In animal cells, gap junctions are formed...

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Estimation of Contact Regions Between Hands and Objects During Human Multi-Digit Grasping
09:41

Estimation of Contact Regions Between Hands and Objects During Human Multi-Digit Grasping

Published on: April 21, 2023

Maximum contact map overlap revisited.

Rumen Andonov1, Noël Malod-Dognin, Nicola Yanev

  • 1INRIA Rennes-Bretagne Atlantique, University of Rennes 1, Rennes, France. Rumen.Andonov@irisa.fr

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|January 8, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces an advanced integer programming model and branch-and-bound algorithm for calculating maximum contact map overlap (CMO) in 3D protein structures, significantly improving large-scale comparison efficiency and accuracy.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Algorithm development

Background:

  • Maximum contact map overlap (CMO) is crucial for quantifying 3D protein structure similarity.
  • Existing algorithms for CMO are computationally intensive and limited for large-scale analyses.

Purpose of the Study:

  • To develop a novel and efficient computational approach for CMO calculation.
  • To enable accurate and scalable comparison of large protein structure datasets.

Main Methods:

  • Formulation of a new integer programming model for CMO.
  • Development of an exact branch-and-bound algorithm utilizing Lagrangian relaxation for bounding.
  • Validation on benchmark datasets (Skolnick set) and a newly constructed large-scale dataset (300 protein domains).

Main Results:

  • The proposed algorithm significantly outperforms existing exact methods on benchmark datasets.
  • Numerous previously unsolved CMO instances were successfully resolved.
  • A large-scale comparison of 44,850 protein pairs yielded results in high agreement with the SCOP database.

Conclusions:

  • The novel integer programming model and algorithm offer a substantial advancement in CMO computation.
  • The approach enables efficient and accurate large-scale 3D protein structure similarity analysis.
  • This work provides a powerful tool for protein structure classification and comparison.