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Related Concept Videos

Protein Organization01:13

Protein Organization

Overview
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 Organization01:24

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 Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Related Experiment Video

Updated: Jun 22, 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

Iterative non-sequential protein structural alignment.

Saeed Salem1, Mohammed J Zaki, Christopher Bystroff

  • 1Department of Computer Science, Rensselaer Polytechnic Institute, 110 8th st. Troy, New York 12180, USA. salems@cs.rpi.edu

Journal of Bioinformatics and Computational Biology
|June 10, 2009
PubMed
Summary
This summary is machine-generated.

SNAP is a novel approach for protein structural alignment, improving evolutionary relationship insights. It offers longer alignments with lower root-mean-square deviation (rmsd) than existing methods.

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Last Updated: Jun 22, 2026

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Published on: July 16, 2017

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein structural similarity reveals evolutionary relationships, especially when sequence similarity is low.
  • Accurate structural alignment is crucial for understanding protein function and evolution.

Purpose of the Study:

  • To introduce SNAP (Structural Alignment) as a novel method for non-sequential pair-wise structural alignment.
  • To develop a robust algorithm for constructing both sequential and non-sequential protein alignments.

Main Methods:

  • SNAP employs an iterative two-step process: superposition and alignment, until convergence.
  • A novel greedy algorithm is utilized for constructing alignments.
  • The approach was validated using SISY and RIPC datasets against reference alignments.

Main Results:

  • SNAP generated longer alignments with lower root-mean-square deviation (rmsd) compared to state-of-the-art methods on the CATH database.
  • Protein fold classification using SNAP alignments demonstrated high sensitivity and selectivity.
  • The method was tested on 4410 protein pairs from the CATH database.

Conclusions:

  • SNAP provides a powerful tool for protein structural alignment, enhancing the study of evolutionary relationships.
  • The method's performance in alignment quality and fold classification suggests its utility in structural bioinformatics.
  • SNAP software and datasets are publicly available for further research.