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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.
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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.
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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POSA: a user-driven, interactive multiple protein structure alignment server.

Zhanwen Li1, Padmaja Natarajan1, Yuzhen Ye2

  • 1Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.

Nucleic Acids Research
|May 20, 2014
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Summary
This summary is machine-generated.

The updated Partial Order Structure Alignment (POSA) server enhances protein structure alignment with user-defined anchors and interactive visualization. These features improve alignment accuracy and biological relevance for researchers.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biophysics

Background:

  • Multiple protein structure alignment is crucial for understanding protein function and evolution.
  • Existing tools may lack flexibility and user guidance in complex alignment tasks.
  • The Partial Order Structure Alignment (POSA) server was previously introduced in 2005.

Purpose of the Study:

  • To introduce significant improvements to the POSA server for enhanced multiple protein structure alignment.
  • To provide users with tools for incorporating biological insights into the alignment process.
  • To offer advanced interactive visualization options for analyzing alignment results.

Main Methods:

  • Implementation of a new interface for users to define anchor segments in input structures.
  • Development of interactive visualization tools for simultaneous or synchronized viewing of superposed structures.
  • Integration of user-controlled rotation and detailed examination of structural similarities and differences.

Main Results:

  • The enhanced POSA server allows for user-guided, biologically relevant protein structure alignments.
  • Interactive visualization facilitates clearer identification of structural similarities and differences.
  • The server remains free, open-access, with optional user registration for result storage.

Conclusions:

  • The updated POSA server offers a more intuitive and powerful platform for multiple protein structure alignment.
  • User-defined anchors and advanced visualization significantly improve the alignment process and result interpretation.
  • POSA continues to be a valuable resource for structural bioinformatics research.