Related Experiment Video
Updated: May 11, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Network properties of decoys and CASP predicted models: a comparison with native protein structures
S Chatterjee1, S Ghosh, S Vishveshwara
1Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560012, India.
Molecular Biosystems
|May 23, 2013
Summary
Protein Structure Networks (PSNs) combined with Support Vector Machines (SVM) accurately distinguish native protein structures from models. This novel approach assesses protein models independently, aiding in structure validation.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Machine Learning in Biochemistry
Background:
- Protein sequence space is vast, yet protein structure space is finite, suggesting proteins adopt known folds.
- Accurate protein structure prediction remains challenging, with a key difficulty being distinguishing native structures from computational models (decoys).
- Existing sequence-structure correlation data has not fully resolved the protein structure prediction problem.
Purpose of the Study:
- To rigorously investigate Protein Structure Networks (PSNs) for detecting native protein structures from decoys.
- To develop a general metric for distinguishing native structures from models using network parameters and machine learning.
- To validate the developed approach on recent protein structure predictions, such as those from CASP10.
Main Methods:
- Analysis of ninety-four parameters derived from Protein Structure Network (PSN) studies.
- Optimal combination of PSN parameters with Support Vector Machines (SVM) to create a classification metric.
- Exploration of transition profiles at varying non-covalent interaction strengths and application to CASP10 models.
Main Results:
- A combined PSN-SVM approach achieved a 94.11% accuracy in distinguishing native protein structures from decoys.
- Transition profiles at different non-covalent interaction strengths were identified as a significant parameter by SVM.
- The SVM-trained algorithm successfully applied to recent CASP10 predicted models.
Conclusions:
- Protein Structure Networks offer a novel, generalizable method for assessing protein structure models independently of reference structures.
- The developed PSN-SVM metric provides a valuable tool for validating predicted protein structures.
- A freely available web-server has been developed to implement this structure validation approach.
Related Concept Videos
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...