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Related Concept Videos

Temperature Dependent Deformation01:12

Temperature Dependent Deformation

In a nonhomogeneous rod made up of steel and brass, restrained at both ends and subjected to a temperature change, several steps are involved in calculating the stress and compressive load. Due to the problem's static indeterminacy, one end support is disconnected, allowing the rod to experience the temperature change freely. Next, an unknown force is applied at the free end, triggering deformations in the rod's steel and brass portions. These deformations are then calculated and added together...
Deformation of Member under Multiple Loadings01:11

Deformation of Member under Multiple Loadings

When a rod is made of different materials or has various cross-sections, it must be divided into parts that meet the necessary conditions for determining the deformation. These parts are each characterized by their internal force, cross-sectional area, length, and modulus of elasticity. These parameters are then used to compute the deformation of the entire rod.
In the case of a member with a variable cross-section, the strain is not constant but depends on the position. The deformation of an...
Plastic Deformations01:19

Plastic Deformations

Plastic deformation represents a fundamental concept in materials science, which explains the irreversible change in the shape of a material when it experiences stress beyond its elastic capability. This phenomenon is important in structural engineering, especially in designing and analyzing cantilever beams—structures that are securely fixed at one end and bear loads at the opposite end. When these beams are subjected to loads within their elastic range, they will return to their original...
Plastic Deformations01:14

Plastic Deformations

It is essential to understand how structural members behave under plastic deformation when the bending stress exceeds the material's yield strength. This state of deformation permanently alters the shape of the member, in contrast to the linear elastic behavior observed before yielding. The strain at any point in the member is expressed in terms of maximum strain. Notably, the neutral axis, which coincides with the centroid during elastic bending, shifts away from the centroid under plastic...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Deformation of a Beam under Transverse Loading01:15

Deformation of a Beam under Transverse Loading

Understanding beam deflection, particularly for indeterminate beams with overhanging segments and multiple concentrated loads, is crucial for ensuring structural integrity and functionality. The process begins with constructing an accurate free-body diagram, which helps identify the forces and moments acting on the beam. This diagram is vital for visualizing how bending moments vary along the beam's length, influencing its curvature.
The insights from the bending moment diagram extend to...

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Related Experiment Video

Updated: Jul 17, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

DFprot: a webtool for predicting local chain deformability.

José Ignacio Garzón1, Julio Kovacs, Ruben Abagyan

  • 1Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.

Bioinformatics (Oxford, England)
|February 6, 2007
PubMed
Summary

DFprot predicts protein main-chain deformability using normal-mode analysis. This tool provides a rapid, quantitative estimate of protein flexibility for researchers without specialized computational expertise.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein flexibility is crucial for biological function.
  • Predicting deformability from static structures is challenging.
  • Existing methods may require specialized expertise.

Purpose of the Study:

  • To develop a user-friendly web server for predicting protein main-chain deformability.
  • To provide a quantitative measure of residue-level flexibility.
  • To enable rapid analysis of protein structures for non-specialists.

Main Methods:

  • Utilizes normal-mode analysis (NMA) on uploaded protein conformations.
  • Automates the NMA process for ease of use.
  • Calculates deformability at each residue of the protein structure.

Main Results:

  • DFprot successfully predicts main-chain deformability.
  • The server offers a quantitative approximation of protein flexibility.
  • Provides an efficient interface for rapid structural analysis.

Conclusions:

  • DFprot serves as a valuable tool for assessing protein flexibility.
  • Simplifies the process of obtaining deformability information from protein structures.
  • Facilitates the study of protein dynamics for a broader scientific audience.