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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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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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

PredUs: a web server for predicting protein interfaces using structural neighbors.

Qiangfeng Cliff Zhang1, Lei Deng, Markus Fisher

  • 1Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, USA.

Nucleic Acids Research
|May 26, 2011
PubMed
Summary
This summary is machine-generated.

PredUs predicts protein-protein interfaces by mapping contacts from known structures. This web server aids researchers in identifying potential interfacial residues for proteins.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure analysis

Background:

  • Protein-protein interactions are crucial for cellular functions.
  • Accurate prediction of protein-protein interfaces is essential for understanding biological processes.
  • Existing methods may lack interactive features for hypothesis-driven analysis.

Purpose of the Study:

  • To introduce PredUs, an interactive web server for predicting protein-protein interfaces.
  • To provide a user-friendly tool for identifying potential interfacial residues.
  • To enable researchers to tailor predictions based on specific hypotheses.

Main Methods:

  • Residue-level interface prediction using a support vector machine (SVM).
  • Contact mapping from structural neighbors of query proteins to their surface residues.
  • Interactive visualization of results using a molecular viewer.

Main Results:

  • The PredUs server successfully identifies potential interfacial residues.
  • The method leverages structural information from homologous proteins.
  • Interactive features allow for customized analysis and hypothesis testing.

Conclusions:

  • PredUs offers an effective and interactive approach for protein-protein interface prediction.
  • The web server facilitates structural bioinformatics research.
  • The tool supports hypothesis-driven investigation of protein interactions.