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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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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.
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...
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Molecular Models02:00

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Chemical Shift: Internal References and Solvent Effects01:17

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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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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Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin
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MolProbity: More and better reference data for improved all-atom structure validation.

Christopher J Williams1, Jeffrey J Headd1, Nigel W Moriarty2

  • 1Department of Biochemistry, Duke University, Durham, NC, 27710, USA.

Protein Science : a Publication of the Protein Society
|October 26, 2017
PubMed
Summary
This summary is machine-generated.

The MolProbity web service now offers enhanced macromolecular model validation. Updates include improved infrastructure, new validation criteria, and better integration with the Phenix software for structural biology research.

Keywords:
Asn/Gln/His flipCCTBXCaBLAMTop8000all-atom contact analysiscis non-prolineelectron-cloud hydrogen position

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biochemistry

Background:

  • The MolProbity web service provides essential validation tools for macromolecular models.
  • Previous versions of MolProbity underwent significant updates in 2010.
  • Continuous improvement of validation services is crucial for structural biology.

Purpose of the Study:

  • To detail the recent updates and improvements to the MolProbity macromolecular model validation services.
  • To highlight new features and infrastructure enhancements since 2010.
  • To emphasize the integration of MolProbity validation within the Phenix software system.

Main Methods:

  • Rewriting Java utilities to Python within the open-source CCTBX/Phenix framework.
  • Establishing a complete MolProbity mirror site and utilizing GitHub for open-source code and datasets.
  • Developing and implementing new validation criteria, including CaBLAM analysis and improved distance/radii parameters.

Main Results:

  • Enhanced long-term maintainability and integration of MolProbity validation within Phenix.
  • Improved accuracy of heavy-atom-to-hydrogen distances and van der Waals radii.
  • Introduction of new validation checks for format irregularities, Ramachandran and rotamer outliers, secondary structure, and peptide bond conformations.

Conclusions:

  • MolProbity validation services have been significantly updated, enhancing their utility for structural biology.
  • The integration with Phenix and open-source development practices improve accessibility and maintainability.
  • Continued application of MolProbity leads to ongoing improvements in the quality of newly deposited macromolecular structures.