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Related Concept Videos

Potential Energy00:52

Potential Energy

The energy stored by a structure and location of matter in space is called potential energy. For instance, raising a kettlebell changes its spatial location and increases its potential energy. Similarly, a stretched rubber band contains potential energy which, under certain conditions, can be converted into other forms of energy, such as kinetic energy.
Chemical bonds that form attractive forces between atoms also contain potential energy, called chemical energy. When a chemical reaction...
Potential Energy01:09

Potential Energy

A conservative force, such as a gravitational or elastic force, gives the body the capacity to do work. This capacity, measured as the potential energy, depends on the body's location or “position” relative to a fixed reference position or datum. The gravitational potential energy is considered zero at the reference point. Suppose a body is located at some vertical distance above a fixed horizontal reference or datum. In that case, the weight of the body has positive gravitational potential...
Thermodynamic Potentials01:26

Thermodynamic Potentials

Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...
Potential-Energy Criterion for Equilibrium01:16

Potential-Energy Criterion for Equilibrium

Potential energy or potential function plays an essential role in determining the stability of a mechanical system. If a system is subjected to both gravitational and elastic forces, the potential function of the system can be expressed as the algebraic sum of gravitational and elastic potential energy. If the system is in equilibrium and is displaced by a small amount, then the work done on the system equals the negative of the change in the system's potential energy from the initial to the...
Cell Potential and Free Energy02:58

Cell Potential and Free Energy

Thermodynamics of a Redox Reaction
Thermodynamics is the branch of physics dealing with the relationship between heat and other forms of energy. In an electrochemical cell, chemical energy is converted into electrical energy.
Thus, a link can be predicted between cell potential, free energy change, and the equilibrium constant for the reaction. Cell potential can also be measured as the oxidant or the reducing strength, and similar acid-base strength measures are reflected in equilibrium...
Force and Potential Energy in One Dimension01:13

Force and Potential Energy in One Dimension

Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...

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Related Experiment Video

Updated: Jun 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials.

Yaping Feng1, Andrzej Kloczkowski, Robert L Jernigan

  • 1Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011-0320, USA.

BMC Bioinformatics
|February 19, 2010
PubMed
Summary
This summary is machine-generated.

A new online server provides easy access to knowledge-based potentials for calculating protein structure energies. This tool simplifies protein modeling and design by making complex potentials readily available for researchers.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • Knowledge-based potentials are crucial for various protein structure analyses, including fold recognition and prediction.
  • Despite their utility, these potentials are often not easily accessible online, hindering widespread use.
  • Existing methods lack a centralized, user-friendly platform for accessing and applying diverse potentials.

Purpose of the Study:

  • To develop and provide an accessible online server for utilizing various knowledge-based potentials.
  • To enable automated computation of protein structure energies using user-supplied models.
  • To facilitate protein structure prediction, ligand binding analysis, and protein design research.

Main Methods:

  • Implementation of a web server featuring a user-friendly interface.
  • Integration of multiple potential types, including four-body, short-range, and 23 two-body potentials.
  • Support for PDB file uploads for protein structure data and email delivery of results.

Main Results:

  • A functional web server, "Potentials 'R' Us," is now available online.
  • The server allows users to select and apply various potentials for energy calculations.
  • Automated energy computation for user-submitted protein models is successfully implemented.

Conclusions:

  • The "Potentials 'R' Us" server offers a freely accessible tool for protein energy estimation.
  • It centralizes existing and future protein coarse-grained potentials for broader research application.
  • The platform simplifies the process of evaluating multiple structural models efficiently.