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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.
Multicompartment Models: Overview01:14

Multicompartment Models: Overview

Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
Three-Compartment Open Model01:06

Three-Compartment Open Model

The three-compartment open model is a pharmacokinetic model used to describe the distribution and elimination of drugs following extravascular administration. It comprises a central compartment representing the plasma and two peripheral compartments. The highly perfused peripheral compartment represents organs and tissues with a rich blood supply, such as the liver, kidneys, and lungs. The scarcely perfused peripheral compartment represents tissues with lower blood supply, such as adipose...
Mechanistic Models: Overview of Compartment Models01:21

Mechanistic Models: Overview of Compartment Models

Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
Modeling and Similitude01:12

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Scaled modeling is a fundamental technique in engineering, enabling the study of large and complex systems by creating smaller, manageable replicas that recreate critical characteristics of the original. In hydrology and civil infrastructure, for example, scaled models of dams help analyze water flow, turbulence, and pressure. This method allows for accurate predictions of real-world behavior within a controlled environment, significantly reducing the cost and time involved in full-scale...

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Related Experiment Video

Updated: May 28, 2026

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

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

UCSF Chimera, MODELLER, and IMP: an integrated modeling system.

Zheng Yang1, Keren Lasker, Dina Schneidman-Duhovny

  • 1Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

Journal of Structural Biology
|October 4, 2011
PubMed
Summary

UCSF Chimera now integrates advanced tools for macromolecular complex modeling. This includes comparative modeling, fitting components into density maps, and analyzing scattering data for structural insights.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Last Updated: May 28, 2026

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

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Published on: December 25, 2021

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Macromolecular complex structural modeling requires robust visualization tools.
  • Integrating diverse modeling approaches enhances accuracy and efficiency.

Purpose of the Study:

  • To present the integration of multiple modeling tools within UCSF Chimera.
  • To provide a comprehensive platform for structural analysis of macromolecular complexes.

Main Methods:

  • Integration of MODELLER for comparative modeling.
  • Implementation of IMP MultiFit for fitting multiple components into electron microscopy density maps.
  • Incorporation of IMP FoXS for small-angle X-ray scattering (SAXS) profile computation and fitting.
  • Utilizing Chimera for assessing amino acid sidechain conformations.

Main Results:

  • UCSF Chimera now offers a unified environment for various structural modeling tasks.
  • The integrated tools facilitate simultaneous fitting of multiple components into experimental data.
  • Enhanced capabilities for analyzing SAXS data and sidechain conformations are provided.

Conclusions:

  • The integration significantly enhances the utility of UCSF Chimera for structural modeling.
  • This comprehensive platform supports detailed analysis from comparative modeling to experimental data fitting.