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Related Concept Videos

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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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...
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Multi-pass Transmembrane Proteins and β-barrels01:09

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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...
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Protein-Protein Interfaces02:04

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Protein-protein Interfaces02:04

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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...
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Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

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The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
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Tail-anchoring of Proteins in the ER Membrane01:45

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Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
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Related Experiment Video

Updated: Jul 24, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

Lee-Shin Chu1, Jeffrey A Ruffolo2, Ameya Harmalkar1

  • 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

Biorxiv : the Preprint Server for Biology
|July 10, 2023
PubMed
Summary

GeoDock is a new deep learning method for protein-protein docking that predicts complex structures quickly and accurately. It handles flexible proteins and outperforms existing methods in speed and success rate for structure-based virtual screening.

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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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Last Updated: Jul 24, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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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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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Machine learning in drug discovery

Background:

  • Traditional protein-protein docking is slow due to extensive sampling and re-ranking.
  • Current deep learning docking methods are fast but have low success rates and assume rigid structures.
  • Rigid docking fails to account for binding-induced conformational changes crucial for allosteric inhibition.

Conclusions:

  • GeoDock offers a significant advancement in fast and accurate protein-protein docking.
  • The architecture provides a foundation for predicting backbone flexibility in protein complexes.
  • The method shows promise for structure-based virtual screening and understanding allosteric mechanisms.