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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: May 19, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Producing high-accuracy lattice models from protein atomic coordinates including side chains.

Martin Mann1, Rhodri Saunders, Cameron Smith

  • 1Bioinformatics, University of Freiburg, Georges-Köhler Allee 106, 79110 Freiburg im Breisgau, Germany.

Advances in Bioinformatics
|August 31, 2012
PubMed
Summary
This summary is machine-generated.

LatFit is a new computational tool for creating accurate protein models on lattices, offering both backbone-only and side-chain models. It provides faster fitting and low deviation, advancing lattice protein modeling research.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: May 19, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein modeling

Background:

  • Lattice models simplify protein structure analysis, enabling computationally feasible evaluations.
  • Existing tools for lattice protein fitting are limited, with only one backbone-only option available.
  • Accurate lattice models are crucial for understanding protein folding and refinement.

Purpose of the Study:

  • To introduce LatFit, a novel tool for generating high-accuracy on-lattice protein models.
  • To enable the creation of both backbone-only and backbone-side-chain models on user-defined lattices.
  • To present a comprehensive study on lattice model quality, including side chains.

Main Methods:

  • LatFit implements both coordinate RMSD and a new distance RMSD-optimisation fitting procedure.
  • The tool was tested on a nonredundant set of high-resolution proteins from the SCOP database.
  • Evaluations were performed on 3D cubic, face-centred cubic (FCC), and knight's walk lattices.

Main Results:

  • LatFit demonstrated favorable fitting speeds compared to existing methods.
  • Both backbone-only and backbone-side-chain models exhibited low deviation from original protein data (~1.5 Å RMSD in FCC lattice).
  • This study represents the first comprehensive analysis of lattice quality for on-lattice models incorporating side chains.

Conclusions:

  • LatFit is the sole available tool for generating on-lattice protein models with side chains.
  • The tool achieves high accuracy and efficiency in lattice protein modeling.
  • LatFit advances the field by enabling detailed studies of protein structure on various lattices.