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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.
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.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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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Updated: Jun 10, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

Minimalist models for proteins: a comparative analysis.

Valentina Tozzini1

  • 1NEST, Istituto Nanoscienze - CNR Scuola Normale Superiore, Piazza San Silvestro 12, I-56127 Pisa, Italy. tozzini@nest.sns.it

Quarterly Reviews of Biophysics
|August 17, 2010
PubMed
Summary
This summary is machine-generated.

Coarse-grained (CG) models simplify complex biopolymer simulations for large systems and long timescales. This review focuses on minimalist protein models, offering guidelines for developing accurate and predictive CG models.

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Last Updated: Jun 10, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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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
  • Biophysics
  • Molecular modeling

Background:

  • Modern molecular biology requires simulating nano- to micro-sized biomolecular systems over microsecond timescales.
  • Atomic-level simulations face limitations in accessing these large size and timescale regimes.
  • Coarse-graining (CG) offers a computational strategy to overcome these limitations.

Purpose of the Study:

  • To review and compare features, applications, and performance of various CG models for proteins.
  • To focus on minimalist CG models that retain secondary structure information while minimizing degrees of freedom.
  • To provide guidelines for developing improved minimalist CG models.

Main Methods:

  • Review and comparative analysis of existing CG models for proteins.
  • Focus on minimalist models using one or a few beads per amino acid.
  • Analysis of force field (FF) terms, functional forms, and parameterization procedures.

Main Results:

  • Building effective CG models requires balancing transferability/predictive power with structural accuracy.
  • Optimizing FF terms and parameterization strategies can enhance model performance.
  • Regularities in parameter values and FF terms exist across different minimalist models.

Conclusions:

  • Minimalist CG models offer a viable approach for large-scale, long-timescale biopolymer simulations.
  • Careful selection of FF components and parameterization methods is crucial for model development.
  • A generic phase diagram can guide the creation of next-generation minimalist CG models with enhanced predictive power and accuracy.