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Related Concept Videos

Protein Organization01:24

Protein Organization

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.
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Protein Families02:47

Protein Families

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 locations, protein...
Protein Families02:47

Protein Families

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 locations, protein...

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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MODBASE, a database of annotated comparative protein structure models and associated resources.

Ursula Pieper1, Narayanan Eswar, Ben M Webb

  • 1Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.

Nucleic Acids Research
|October 25, 2008
PubMed
Summary
This summary is machine-generated.

MODBASE provides a comprehensive database of over 5 million annotated comparative protein structure models. This resource aids researchers by offering reliable protein models and tools for on-demand model calculation and analysis.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein modeling

Background:

  • Comparative protein modeling is crucial for understanding protein function and structure.
  • Automated pipelines are essential for generating large-scale protein model databases.

Purpose of the Study:

  • To present MODBASE, a large-scale database of annotated comparative protein structure models.
  • To highlight the integrated resources and on-demand modeling capabilities offered by MODBASE.

Main Methods:

  • Utilizing the MODPIPE automated modeling pipeline, primarily with MODELLER software.
  • Employing rigorous criteria for fold assignment, sequence-structure alignment, and model assessment.
  • Integrating diverse databases for alignments, ligand binding sites, and mutation data.

Main Results:

  • MODBASE contains over 5.1 million reliable models for nearly 1.6 million unique protein sequences.
  • Models are included only if based on statistically significant alignments or assessed as having the correct fold.
  • On-demand model calculation is available via the MODWEB modeling server.

Conclusions:

  • MODBASE serves as a valuable resource for structural biology and bioinformatics research.
  • The database facilitates protein structure prediction, analysis, and functional inference.
  • Integration with other databases enhances the utility of MODBASE for diverse biological investigations.