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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...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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,...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Gene Families01:57

Gene Families

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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Related Experiment Video

Updated: Jun 18, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

GWIDD: Genome-wide protein docking database.

Petras J Kundrotas1, Zhengwei Zhu, Ilya A Vakser

  • 1Department of Molecular Biosciences, The University of Kansas, Center for Bioinformatics and Lawrence, KS 66047, USA.

Nucleic Acids Research
|November 11, 2009
PubMed
Summary
This summary is machine-generated.

The Genome-Wide Docking Database provides structural insights into protein-protein interactions across all life forms. This resource integrates experimental and modeled data for genome-scale studies.

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Last Updated: Jun 18, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Understanding protein-protein interactions is crucial for deciphering molecular mechanisms of life.
  • Structural information provides key insights into the function and regulation of biological processes.

Purpose of the Study:

  • To present the Genome-Wide Docking Database (GWIDD) as an integrated resource for studying protein-protein interactions.
  • To provide a comprehensive collection of experimental and modeled 3D structures for protein interactions across diverse organisms.

Main Methods:

  • Integration of experimentally determined protein structures.
  • Application of computational docking techniques to model protein interactions.
  • Organization of data within a relational database structure.

Main Results:

  • The database contains 25,559 experimental and modeled 3D structures.
  • Data covers 771 organisms, from viruses to humans.
  • A user-friendly interface allows exploration by multiple parameters.

Conclusions:

  • GWIDD offers a valuable resource for genome-scale structural studies of protein-protein interactions.
  • The database facilitates interactive exploration and download of structural data.
  • This resource supports research in molecular biology and structural biology.