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Related Concept Videos

Protein Families02:47

Protein Families

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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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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,...
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Conserved Binding Sites

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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...
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Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Related Experiment Video

Updated: Apr 23, 2026

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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NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote

Richa Mudgal1, Sankaran Sandhya2, Gayatri Kumar3

  • 1IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, Karnataka, India.

Nucleic Acids Research
|September 29, 2014
PubMed
Summary

The NrichD database uses computationally designed protein sequences to bridge gaps in natural sequence data, improving the detection of distant protein relationships. This approach enhances standard search methods by filling voids in protein sequence space.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Detecting remote protein relationships is challenging without structural evidence or intermediate sequences.
  • Computational design of artificial intermediary sequences can fill gaps in protein sequence space.
  • Enriching natural sequence databases with artificial sequences can improve remote relationship detection.

Purpose of the Study:

  • To introduce the NrichD database, a resource of computationally designed protein-like sequences.
  • To demonstrate the utility of artificial intermediary sequences in enhancing remote protein relationship detection.
  • To enrich existing structural and functional databases (SCOP, Pfam) with artificial sequences.

Main Methods:

  • Generation of computationally designed protein-like sequences.
  • Augmentation of natural sequence databases with artificial sequences.
  • Large-scale assessment of the performance improvement in sequence search methods.
  • Enrichment of SCOP and Pfam databases with artificial intermediary sequences.

Main Results:

  • The NrichD database contains over 3.6 million artificial sequences.
  • These sequences bridge 27,882 family pairs across 374 SCOP folds.
  • The inclusion of artificial sequences improves the detection of remote protein relationships.
  • The enriched SCOP and Pfam databases are now available.

Conclusions:

  • Computationally designed artificial intermediary sequences are effective for establishing remote protein relationships.
  • NrichD provides a valuable resource for bioinformatics research.
  • The approach enhances the capabilities of standard sequence search tools.