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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.
Molecular Models02:00

Molecular Models

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.
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...
Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

MMDB: 3D structures and macromolecular interactions.

Thomas Madej1, Kenneth J Addess, Jessica H Fong

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. madej@ncbi.nlm.nih.gov

Nucleic Acids Research
|December 3, 2011
PubMed
Summary
This summary is machine-generated.

The Molecular Modeling Database (MMDB) now offers enhanced access to protein three-dimensional (3D) structures and interactions. These improvements integrate 3D structure data with sequences and chemical information, making it a more valuable resource for researchers.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Approximately 60% of protein sequences in databases can be linked to known three-dimensional (3D) structures.
  • Protein 3D structure data is an underutilized resource for understanding protein function and families.
  • Access to integrated biological data is crucial for diverse research fields.

Purpose of the Study:

  • To present enhancements in the Molecular Modeling Database (MMDB) for improved data presentation.
  • To facilitate access to biologically relevant protein complexes and molecular interactions.
  • To bridge the gap between 3D structure data and other biological information.

Main Methods:

  • Enhancements to the Molecular Modeling Database (MMDB) and its data presentation.
  • Integration with NCBI's Entrez search and retrieval system.
  • Mirroring contents of the Protein Data Bank.
  • Linking protein 3D structure data with sequence data, classification resources, and PubChem.
  • Utilizing the VAST algorithm for structural alignments.
  • Employing the Cn3D molecular graphics viewer for visualization.

Main Results:

  • MMDB now tightly integrates protein 3D structure data with sequence data, classification resources, and PubChem.
  • A complete set of pre-computed structural alignments from the VAST algorithm is provided.
  • Visualization tools for 3D structure and structure/sequence alignment are available via Cn3D.
  • Enhanced access to biologically relevant complexes and molecular interactions is facilitated.

Conclusions:

  • The enhanced MMDB provides a more comprehensive and accessible resource for exploring protein 3D structures.
  • Integration with other NCBI resources and PubChem broadens the utility for structural biologists, molecular biologists, and chemists.
  • These improvements aim to increase the utilization of 3D structure data in biological research.