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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.
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
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...
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...
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...
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...

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Related Experiment Video

Updated: Jun 3, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Smolign: a spatial motifs-based protein multiple structural alignment method.

Hong Sun1, Ahmet Sacan, Hakan Ferhatosmanoglu

  • 1The Ohio State University, Columbus.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|April 6, 2011
PubMed
Summary
This summary is machine-generated.

A new protein multiple structural alignment (MSTA) method improves discovery of shared motifs. This robust algorithm enhances functional annotation and drug design by aligning similar protein structures, even with low sequence similarity.

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Last Updated: Jun 3, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Biochemistry

Background:

  • Effective protein multiple structural alignment (MSTA) is crucial for identifying biologically significant structural motifs.
  • Current MSTA methods often rely on pairwise comparisons, leading to suboptimal alignments, particularly for proteins with low similarity.
  • Accurate MSTA aids in functional annotation and drug design.

Purpose of the Study:

  • To introduce a novel strategy for protein multiple structural alignment (MSTA).
  • To develop a sensitive and robust automated algorithm for MSTA.
  • To improve the detection of similarities among protein structures, even under low similarity conditions.

Main Methods:

  • A contact-window based motif library is constructed from protein structural data.
  • Common alignment seeds are discovered and extended from this library.
  • Optimal superimposition of multiple structures is achieved using an enhanced partial order curve comparison method based on these seeds.

Main Results:

  • The novel strategy enables simultaneous detection of multiple correspondences and global alignment capture.
  • The method supports flexible alignments, offering enhanced sensitivity and robustness.
  • The new approach outperforms popular MSTA methods on diverse protein structure datasets with varying similarity levels.

Conclusions:

  • The developed MSTA strategy provides superior alignment results compared to existing methods.
  • The algorithm effectively identifies structural similarities in proteins, even with low sequence identity.
  • A web-based tool and executable are available for broader application and validation.