Related Experiment Video
Updated: Jun 14, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
I-TASSER: a unified platform for automated protein structure and function prediction
Ambrish Roy1, Alper Kucukural, Yang Zhang
1Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
Nature Protocols
|April 3, 2010
Summary
The I-TASSER server predicts protein structure and function from amino acid sequences using threading and assembly simulations. It provides accurate 3D models and functional annotations, aiding biological research.
Area of Science:
- Computational biology
- Structural bioinformatics
- Biochemistry
Background:
- Accurate protein structure and function prediction is crucial for understanding biological processes.
- Existing methods often face limitations in scalability and accuracy.
Purpose of the Study:
- To present the iterative threading assembly refinement (I-TASSER) server, an automated platform for protein structure and function prediction.
- To outline the sequence-to-structure-to-function paradigm employed by I-TASSER.
- To provide guidelines for developing similar online server systems.
Main Methods:
- Utilizes multiple threading alignments to generate initial protein models.
- Employs iterative structural assembly simulations for refining 3D atomic models.
- Infers protein function by structurally matching predicted models with known proteins.
Main Results:
- Generates full-length secondary and tertiary structure predictions.
- Provides functional annotations including ligand-binding sites, Enzyme Commission numbers, and Gene Ontology terms.
- Offers an accuracy estimate based on a confidence score.
Conclusions:
- I-TASSER provides a robust and automated approach for protein structure and function prediction.
- The server's output aids in understanding protein roles and designing further biological studies.
- The presented protocol offers valuable insights for developing advanced bioinformatics servers.
Related Concept Videos
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
02:15Protein 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...
A protein's shape is critical to its function. For example, an enzyme can...
02:15Protein 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...
A protein's shape is critical to its function. For example, an enzyme can...
02:04Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...