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Related Concept Videos

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...
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.

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Related Experiment Video

Updated: May 31, 2026

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

Protein design with fragment databases.

Erik Verschueren1, Peter Vanhee, Almer M van der Sloot

  • 1EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain.

Current Opinion in Structural Biology
|June 21, 2011
PubMed
Summary
This summary is machine-generated.

Computational protein design utilizes structure-based methods and large fragment databases. These databases provide building blocks for designing protein structures and interactions, overcoming scaffold limitations for rational engineering.

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

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Last Updated: May 31, 2026

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
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Published on: June 4, 2021

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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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

Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Structure-based computational methods are crucial for rational protein engineering.
  • Designing novel proteins and their interactions requires detailed structural insights.

Purpose of the Study:

  • To demonstrate the utility of large-scale fragment databases for protein structure design.
  • To highlight the importance of interaction pattern catalogs for designing protein-protein interactions.
  • To showcase advancements and remaining challenges in database-driven computational protein design.

Main Methods:

  • Utilizing large-scale databases of structural fragments as discrete building blocks.
  • Saturating structural alphabets to generate conformational ensembles.
  • Analyzing catalogs of interaction patterns to identify suitable scaffolds.

Main Results:

  • Fragment databases offer a complete set of building blocks for de novo structure design.
  • Structural alphabets, when saturated, effectively sample native structure space.
  • Interaction pattern catalogs address the scarcity of scaffolds in computational interaction design.

Conclusions:

  • Database-driven approaches are powerful tools for computational protein design.
  • Leveraging fragment and interaction databases enables rational engineering of proteins and interactions.
  • Further research is needed to address existing challenges and advance the field.