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Related Concept Videos

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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...
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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

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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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LOMETS: a local meta-threading-server for protein structure prediction.

Sitao Wu1, Yang Zhang

  • 1Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 6604, USA.

Nucleic Acids Research
|May 5, 2007
PubMed
Summary

We developed LOMETS, a local threading meta-server, for rapid protein structure prediction. This automated system improves accuracy by combining multiple threading programs, enhancing tertiary structure modeling.

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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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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Bioinformatics

Background:

  • Protein tertiary structure prediction is crucial for understanding protein function.
  • Existing remote-server meta-servers can be slow and less efficient.
  • Automated methods for generating spatial constraints are needed.

Purpose of the Study:

  • To develop LOMETS, a local threading meta-server for fast and automated protein tertiary structure and spatial constraint predictions.
  • To improve the accuracy of protein structure modeling using a consensus approach.
  • To provide a tool that aids in ab initio protein structure modeling.

Main Methods:

  • Implemented a local computer cluster running nine state-of-the-art threading programs.
  • Generated consensus models from top predictions of individual threading servers.
  • Automatically constructed side-chain and C-alpha contacts and distance maps from threading alignments.

Main Results:

  • LOMETS provides quick generation of initial threading alignments.
  • Consensus models showed a 7% improvement in accuracy (TM-score) over individual servers.
  • Achieved 42% accuracy for side-chain contacts and 61% for C-alpha contacts.
  • Generated long- and short-range distance maps for guiding ab initio modeling.

Conclusions:

  • LOMETS offers a significant improvement in automated protein tertiary structure prediction speed and accuracy.
  • The generated spatial constraints effectively guide ab initio modeling procedures like TASSER.
  • LOMETS is a valuable, freely available resource for the academic research community.