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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Improving Translational Accuracy02:07

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Homologous Recombination

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Updated: Jun 23, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

COMPASS server for homology detection: improved statistical accuracy, speed and functionality.

Ruslan I Sadreyev1, Ming Tang, Bong-Hyun Kim

  • 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA. sadreyev@chop.swmed.edu

Nucleic Acids Research
|May 14, 2009
PubMed
Summary
This summary is machine-generated.

The COMPASS web server now offers improved protein structure prediction and remote sequence similarity detection. Enhanced features include better accuracy, faster performance, and new visualization tools for analyzing protein structures.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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Last Updated: Jun 23, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Remote sequence similarity detection and protein structure prediction are crucial in bioinformatics.
  • Profile-based methods like COMPASS are valuable tools for these tasks.
  • Previous versions of COMPASS have been utilized for analyzing protein sequences and structures.

Purpose of the Study:

  • To introduce the recently improved COMPASS public web server.
  • To highlight key developments including enhanced statistical accuracy, increased speed, and new functional features.
  • To demonstrate the utility of the server for protein structure prediction and analysis.

Main Methods:

  • Utilizing a profile-based approach for sequence similarity detection.
  • Implementing parallel processing for increased computational speed.
  • Developing new visualization tools for local structural region analysis.
  • Applying the COMPASS server to analyze a protein of unknown function from CASP8.

Main Results:

  • The improved COMPASS server demonstrates enhanced statistical accuracy in detecting remote sequence similarity.
  • Parallel implementation significantly increased the speed of COMPASS computations.
  • New visualization features facilitate effective analysis of predicted local structural regions.
  • Successful application in the structural, evolutionary, and functional analysis of a CASP8 target protein.

Conclusions:

  • The updated COMPASS web server provides a more accurate, faster, and user-friendly platform for protein structure prediction and remote homology detection.
  • The new features, particularly visualization tools, enhance the interpretability of COMPASS results.
  • COMPASS remains a powerful tool for advancing structural bioinformatics and understanding protein function.