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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.
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VSEPR Theory for Determination of Electron Pair Geometries
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Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.Two regions of electron density in a diatomic...
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Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...
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An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.

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Updated: Jun 5, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

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Published on: December 25, 2021

SWIFT MODELLER: a Java based GUI for molecular modeling.

Abhinav Mathur1, Shankaracharya, Ambarish S Vidyarthi

  • 1Department of Biotechnology, Birla Institute of Technology, Mesra, 835215 Jharkhand, India.

Journal of Molecular Modeling
|January 25, 2011
PubMed
Summary
This summary is machine-generated.

SWIFT MODELLER simplifies protein structure modeling by automating complex tasks in the MODELLER software. This graphical user interface (GUI) reduces the need for scripting and tedious formatting, making MODELLER more accessible.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • MODELLER is a powerful tool for homology modeling but requires significant expertise in command-line operations and scripting.
  • The complexity of MODELLER's input formatting and output analysis presents a barrier for many researchers.
  • Existing protocols for MODELLER are often cumbersome and time-consuming.

Purpose of the Study:

  • To develop a user-friendly graphical user interface (GUI) for the MODELLER software.
  • To automate the complex formatting, scripting, and data extraction processes involved in homology modeling.
  • To enhance the accessibility and efficiency of protein structure modeling using MODELLER.

Main Methods:

  • Developed SWIFT MODELLER, a GUI designed with homology modeling steps in mind.
  • Integrated automated formatting, scripting, and data extraction functionalities.
  • Incorporated Jmol for interactive 3D structure visualization of Protein Data Bank (PDB) files.

Main Results:

  • SWIFT MODELLER significantly simplifies the use of MODELLER by automating tedious tasks.
  • The GUI requires only the target sequence as input, eliminating manual formatting and scripting.
  • Integrated Jmol provides immediate visualization of generated protein structures.

Conclusions:

  • SWIFT MODELLER drastically reduces the skill level and time required for protein structure modeling.
  • The software enhances usability and efficiency, making MODELLER accessible to a broader range of scientists.
  • This tool streamlines the homology modeling workflow, facilitating faster and easier protein structure determination.