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Related Concept Videos

Conserved Binding Sites01:49

Conserved 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...
Conserved Binding Sites01:49

Conserved 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...
Protein-protein Interfaces02:04

Protein-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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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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

Protein functional sites prediction using modified bio-basis function and quantitative indices.

Pradipta Maji1, Chandra Das

  • 1Machine Intelligence Unit, Indian Statistical Institute, Kolkata, 700 108, India. pmaji@isical.ac.in

IEEE Transactions on Nanobioscience
|January 27, 2011
PubMed
Summary
This summary is machine-generated.

A novel modified bio-basis function kernel improves protein functional site prediction. This method efficiently selects bio-basis strings, enhancing accuracy in protein function studies and drug design.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Machine Learning

Background:

  • Predicting protein functional sites is crucial for understanding protein functions and developing new drugs.
  • Kernel-based pattern recognition algorithms, like support vector machines (SVMs), are powerful tools for this prediction task.

Purpose of the Study:

  • To introduce a new string kernel function, the modified bio-basis function, for improved protein functional site prediction.
  • To present an efficient method for selecting bio-basis strings by integrating the Fisher ratio and degree of resemblance.
  • To propose quantitative indices for evaluating the quality of selected bio-basis strings.

Main Methods:

  • Development of a modified bio-basis function string kernel.
  • Implementation of an efficient bio-basis string selection method combining Fisher ratio and degree of resemblance.
  • Evaluation using quantitative indices and support vector machines on diverse protein datasets.

Main Results:

  • The proposed modified bio-basis function demonstrates effectiveness in protein functional site prediction.
  • The integrated bio-basis string selection method proves efficient and effective.
  • Comparative analysis shows advantages over existing bio-basis functions and selection methods.

Conclusions:

  • The modified bio-basis function and its associated string selection method offer a significant advancement in predicting protein functional sites.
  • This approach enhances the accuracy and efficiency of protein function studies and aids in drug design.
  • The proposed quantitative indices provide a reliable means to assess the quality of selected bio-basis strings.