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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.
The Energies of Atomic Orbitals03:21

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In an atom, the negatively charged electrons are attracted to the positively charged nucleus. In a multielectron atom, electron-electron repulsions are also observed. The attractive and repulsive forces are dependent on the distance between the particles, as well as the sign and magnitude of the charges on the individual particles. When the charges on the particles are opposite, they attract each other. If both particles have the same charge, they repel each other.
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The Arrhenius equation relates the activation energy and the rate constant, k, for chemical reactions. In the Arrhenius equation, k = Ae−Ea/RT, R is the ideal gas constant, which has a value of 8.314 J/mol·K, T is the temperature on the kelvin scale, Ea is the activation energy in J/mole, e is the constant 2.7183, and A is a constant called the frequency factor, which is related to the frequency of collisions and the orientation of the reacting molecules.
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Electronic Structure of Atoms02:28

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An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum numbers:  n, l, ml, and...

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Updated: Jun 8, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Rebecca F Alford1, Andrew Leaver-Fay2, Jeliazko R Jeliazkov3

  • 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.

Journal of Chemical Theory and Computation
|April 22, 2017
PubMed
Summary

The Rosetta biomolecular modeling suite

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Area of Science:

  • Biomolecular modeling
  • Computational biology
  • Structural biology

Background:

  • The Rosetta software suite has been instrumental in addressing complex biological questions and engineering challenges.
  • A key component of Rosetta's effectiveness is its energy function, which models biomolecular conformations.
  • This function is parameterized using data from small molecules and X-ray crystallography.

Purpose of the Study:

  • To describe the mathematical models and physical concepts behind the Rosetta Energy Function 2015 (REF15).
  • To provide guidance on utilizing Rosetta energies for analyzing biomolecular models.
  • To highlight recent advancements extending the energy function's applicability.

Main Methods:

  • Detailed description of the mathematical underpinnings of the REF15 energy function.
  • Explanation of physical concepts guiding the energy function's development.
  • Demonstration of applying Rosetta energies to biomolecular model analysis.

Main Results:

  • The REF15 energy function provides a robust framework for biomolecular modeling.
  • The paper elucidates how to interpret and apply Rosetta energy calculations.
  • Recent updates enhance the function's utility for diverse macromolecules.

Conclusions:

  • REF15 represents a significant advancement in biomolecular modeling energy functions.
  • The described methods enable deeper analysis of biomolecular structures and interactions.
  • The expanded capabilities of REF15 broaden its application across various biological macromolecules.