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Related Concept Videos

Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, 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,...
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...

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Related Experiment Video

Updated: Jun 21, 2026

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

PSPP: a protein structure prediction pipeline for computing clusters.

Michael S Lee1, Rajkumar Bondugula, Valmik Desai

  • 1Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD, USA.

Plos One
|July 17, 2009
PubMed
Summary
This summary is machine-generated.

We developed a standalone software package for computational protein structure prediction. This tool enables high-throughput analysis and overcomes limitations of web servers for unlimited protein structure modeling.

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Last Updated: Jun 21, 2026

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

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Protein structures are essential for understanding biological systems and for drug/vaccine design.
  • A significant gap exists between available protein sequence and structural data.
  • Computational protein structure prediction is crucial for bridging this data gap.

Purpose of the Study:

  • To present a standalone software package for computational protein structure prediction.
  • To enable high-throughput structural genomic applications.
  • To offer a flexible alternative to existing web servers with limitations.

Main Methods:

  • The pipeline integrates over 20 software packages and databases.
  • Protein sequences are divided into domains for prediction.
  • Employs comparative modeling, fold recognition, and ab initio methods.
  • Models are scored using statistical potentials and force fields.
  • Ab initio models are annotated against the SCOP database.
  • Predicts secondary structure, solvent accessibility, and transmembrane helices.

Main Results:

  • The software package performs all three classes of protein structure prediction methodologies.
  • It can be deployed on user-owned high-performance computing clusters.
  • Handles potentially unlimited queries and resource-intensive ab initio predictions.
  • Results are generated in multiple formats (text, tab-delimited, HTML).
  • Successfully applied to study viral and bacterial proteomes.

Conclusions:

  • The standalone pipeline offers greater flexibility and capacity than web servers.
  • Users can leverage their own computing resources for extensive protein structure prediction.
  • Facilitates large-scale structural genomics and proteomic studies.