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Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Protein Organization

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 and Protein Structures

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...

Protein and Protein Structure

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...

Conservation of Protein Domains

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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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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KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

João P G L M Rodrigues¹, Michael Levitt, Gaurav Chopra

¹Department of Structural Biology, 299 Campus Dr W, Fairchild Bldg, Room D100, Stanford University, Stanford, CA 94305, USA.

Nucleic Acids Research

|May 9, 2012

Summary

This summary is machine-generated.

The KoBaMIN web server refines protein structures efficiently using a knowledge-based potential. This computational tool accurately improves protein models, demonstrating top performance in structure prediction challenges.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural bioinformatics
Computational biology
Biochemistry

Background:

Protein structure refinement is crucial for understanding protein function.
Existing methods can be computationally intensive and less accurate.
Accurate protein models are essential for drug discovery and biological research.

Purpose of the Study:

To introduce the KoBaMIN web server for efficient protein structure refinement.
To provide an online tool for improving protein structural models.
To enable assessment of refinement protocol effectiveness.

Main Methods:

Utilizes a knowledge-based potential of mean force for minimization.
Accepts single structures or ensembles in PDB format.
Includes optional stereochemistry optimization with MESHI software.

Main Results:

KoBaMIN demonstrates computational efficiency and accuracy.
The refinement protocol implicitly accounts for solvent and crystal effects.
Benchmarking on CASP7 decoys and top CASP8/CASP9 refinement category performance.

Conclusions:

KoBaMIN offers a fast and accurate protein structure refinement solution.
The web server is a valuable resource for the structural biology community.
Consistent performance across various model quality ranges validates the approach.