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Related Concept Videos

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.
Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Updated: Jun 22, 2026

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

seeMotif: exploring and visualizing sequence motifs in 3D structures.

Darby Tien-Hao Chang1, Ting-Ying Chien, Chien-Yu Chen

  • 1Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C.

Nucleic Acids Research
|May 30, 2009
PubMed
Summary
This summary is machine-generated.

SeeMotif visualizes sequence motifs on protein structures, aiding functional role discovery. This web service helps researchers understand protein functions by integrating sequence and 3D structure data.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Sequence motifs are crucial for identifying protein functions and facilitating sequence annotation.
  • Characterizing novel motifs and their synergistic relationships is essential for advancing molecular biology.
  • The rapid accumulation of 3D protein structures necessitates tools for their effective analysis.

Purpose of the Study:

  • To develop a web service, seeMotif, for interactive visualization of sequence motifs on protein structures.
  • To provide researchers with a tool to simultaneously view multiple motifs across related protein structures.
  • To facilitate the understanding of protein functions by integrating sequence and structural information.

Main Methods:

  • Development of the seeMotif web service with an interactive user interface.
  • Utilizing Protein Data Bank (PDB) structures for motif visualization.
  • Implementation of complementary approaches for structure selection and motif mapping to account for PDB sequence variations.

Main Results:

  • seeMotif enables rapid visualization of sequence motif locations and conformations on protein 3D structures.
  • The service allows simultaneous comparison of motifs across multiple related structures.
  • seeMotif addresses challenges related to shorter PDB sequences and missing residues.

Conclusions:

  • seeMotif provides a valuable resource for exploring and understanding the functional roles of sequence motifs.
  • Integrating sequence and structure data through seeMotif aids in characterizing uncharacterized protein families.
  • This tool supports large-scale genome projects by enhancing protein function prediction and annotation.