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Related Concept Videos

Protein Organization01:24

Protein Organization

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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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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Protein Families02:47

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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...
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Globular and Fibrous Proteins02:21

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Directing Proteins to the Rough Endoplasmic Reticulum01:34

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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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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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Updated: Jul 8, 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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Redocking the PDB.

Florian Flachsenberg1, Christiane Ehrt1, Torben Gutermuth1

  • 1Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany.

Journal of Chemical Information and Modeling
|December 18, 2023
PubMed
Summary
This summary is machine-generated.

We developed JAMDA, an automated workflow for molecular docking in drug design. It achieves a 61.8% success rate on high-quality protein structures, comparable to AutoDock Vina.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Molecular docking is crucial for structure-based drug design (SBDD).
  • Current docking methods often require multiple tools and manual intervention.
  • Automating the docking process can improve efficiency and reduce bias.

Purpose of the Study:

  • To present the JAMDA (JACS Molecular Docking Analysis) preprocessing and docking workflow.
  • To evaluate JAMDA's performance and identify factors influencing its success.
  • To provide a realistic estimate of automated redocking performance.

Main Methods:

  • Developed a fully automated preprocessing and docking workflow (JAMDA).
  • Evaluated JAMDA on binding sites from the Protein Data Bank (PDB).
  • Applied objective structure quality filters to create the PDBScan22-HQ dataset.

Main Results:

  • JAMDA achieved a top-ranked pose within 2 Å RMSD for 30.1% of structures in the PDBScan22 dataset.
  • Success rate increased to 61.8% for the quality-filtered PDBScan22-HQ dataset.
  • JAMDA's performance was comparable to AutoDock Vina on the filtered dataset.

Conclusions:

  • The JAMDA workflow offers an easy-to-use, fully automated solution for molecular docking.
  • Automated preprocessing and quality filtering significantly enhance docking success rates.
  • JAMDA provides a reliable and efficient tool for structure-based drug design.