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Related Concept Videos

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-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...
Insertion of Multi-pass Transmembrane Proteins in the RER01:29

Insertion of Multi-pass Transmembrane Proteins in the RER

The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as G-protein-linked receptors (GPCRs) and...

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Related Experiment Video

Updated: May 21, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Improving transmembrane protein consensus topology prediction using inter-helical interaction.

Han Wang1, Chao Zhang, Xiaohu Shi

  • 1Jilin University, Changchun, China.

Biochimica Et Biophysica Acta
|June 12, 2012
PubMed
Summary
This summary is machine-generated.

A new method, CNTOP, improves alpha helix transmembrane protein topology prediction by combining existing predictors and analyzing inter-helical interactions. This consensus approach enhances accuracy and precisely locates transmembrane helices, outperforming individual and other consensus methods.

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Last Updated: May 21, 2026

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Published on: July 14, 2015

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Genomics

Background:

  • Alpha helix transmembrane proteins (αTMPs) constitute ~30% of genomic ORFs and are vital for biological processes.
  • Experimental structure determination of αTMPs is challenging due to their physicochemical properties.
  • Existing sequence-based topology prediction methods have limitations in accuracy.

Purpose of the Study:

  • To develop a novel, highly accurate consensus topology prediction method for αTMPs.
  • To improve the prediction of transmembrane helix (TMH) location and length.
  • To enhance the understanding of αTMP structure and function through accurate topology prediction.

Main Methods:

  • Developed CNTOP, a consensus topology prediction method for αTMPs.
  • Integrated four leading individual topology predictors.
  • Incorporated predicted inter-helical interactions to refine predictions.
  • Evaluated performance on benchmark and non-redundant polytopic αTMP datasets.

Main Results:

  • CNTOP achieved 87% accuracy on a benchmark dataset and 78% on a non-redundant dataset.
  • The method demonstrated superior topology prediction accuracy compared to individual and existing consensus predictors.
  • CNTOP significantly reduced false positives and false negatives in TMH prediction, improving length and location accuracy.

Conclusions:

  • CNTOP offers a significant advancement in αTMP topology prediction accuracy.
  • The method provides more precise identification of TMHs, aiding structure and function studies.
  • CNTOP represents a valuable tool for bioinformatics and structural biology research.