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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 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 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...
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...
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 10, 2026

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

Evaluating template-based and template-free protein-protein complex structure prediction.

Thom Vreven1, Howook Hwang, Brian G Pierce

  • 1Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, ASC-5th floor room 1069, 368 Plantation St., Worcester, MA 01605, USA. Zhiping.Weng@umassmed.edu.

Briefings in Bioinformatics
|July 3, 2013
PubMed
Summary
This summary is machine-generated.

Template-free docking methods outperformed template-based approaches for protein complex prediction when given equal prediction opportunities. Integrating diverse prediction methods may yield superior results for protein-protein complex structures.

Keywords:
COTHPRISMZDOCKprotein–protein dockingprotein–protein structuretemplate-based prediction

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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

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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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
06:50

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

Published on: January 26, 2024

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Accurate prediction of protein-protein complex structures is crucial for understanding biological processes.
  • Both template-based and template-free (docking) methods are employed for this prediction task.

Purpose of the Study:

  • To compare the performance of template-free docking and template-based methods in predicting protein-protein complex structures.
  • To identify the strengths and weaknesses of each prediction strategy.

Main Methods:

  • Evaluated template-based methods: threading (COTH) and structural alignment (PRISM).
  • Assessed template-free docking method (ZDOCK).
  • Compared performance under different prediction number constraints.

Main Results:

  • Template-based methods (COTH, PRISM) showed similar performance.
  • Docking (ZDOCK) outperformed template-based methods when allowed an equal number of predictions.
  • Template-based methods excelled with complexes involving conformational changes.
  • Threading and docking methods were superior for enzyme-inhibitor complex prediction.

Conclusions:

  • No single method consistently identifies near-native predictions.
  • Integrating results from diverse prediction approaches (docking, threading, alignment) is a promising strategy for improving protein complex structure prediction accuracy.