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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...
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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
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...

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Related Experiment Video

Updated: Jul 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

[Computational method for prediction of protein functional sites using specificity determinants].

O V Kalinina, R B Rassel, A B Rakhmaninova

    Molekuliarnaia Biologiia
    |March 27, 2007
    PubMed
    Summary

    Computational methods for protein function annotation are crucial. A new method, SDPsite, accurately predicts protein functional sites by identifying specificity determinants, aiding experimental studies.

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    Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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    Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

    Published on: July 14, 2015

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Structural Biology

    Background:

    • Experimental protein function annotation faces limitations due to vast sequence data.
    • In silico annotation is vital for prioritizing experimental validation.
    • Predicting protein functional sites is essential for understanding biological roles.

    Purpose of the Study:

    • To introduce SDPsite, a novel computational method for predicting protein functional sites.
    • To leverage protein specificity determinants for accurate functional site prediction.
    • To provide a tool that aids in the interpretation of protein sequence data.

    Main Methods:

    • SDPsite utilizes protein sequence alignments and phylogenetic trees as input.
    • The algorithm identifies conserved positions and specificity determinants.
    • Predicted sites are mapped to 3D structures, and clusters are analyzed.

    Main Results:

    • SDPsite predictions show strong agreement with experimental data.
    • The method outperforms several existing functional site prediction tools.
    • The tool successfully identifies conserved positions and specificity determinants.

    Conclusions:

    • SDPsite offers a reliable and effective approach for in silico protein functional site prediction.
    • The method enhances the efficiency of experimental functional annotation.
    • SDPsite is a valuable resource for the bioinformatics and structural biology communities.