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Related Concept Videos

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...
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...
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 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...
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...
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...

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LigAlign: flexible ligand-based active site alignment and analysis.

Abraham Heifets1, Ryan H Lilien

  • 1Department of Computer Science, Univ. of Toronto, Toronto, Ontario, Canada.

Journal of Molecular Graphics & Modelling
|August 18, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces LigAlign, a novel system for flexible ligand alignment. LigAlign accurately analyzes protein-ligand interactions by considering ligand flexibility, revealing conserved structural motifs missed by rigid alignment methods.

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Ligand-based active site alignment is crucial for analyzing protein-ligand complexes.
  • Current methods often overlook ligand flexibility, treating them as rigid structures.
  • This limitation hinders accurate structural analysis and motif identification.

Purpose of the Study:

  • To develop an automated system, LigAlign, for flexible ligand alignment and analysis.
  • To improve the accuracy of structural analysis in protein-ligand interactions.
  • To identify conserved structural motifs not detectable by rigid alignment.

Main Methods:

  • Implementation of LigAlign, an automated system for flexible ligand alignment.
  • Comparison of LigAlign's flexible alignment results with existing rigid alignment tools.
  • Validation of LigAlign's ability to perform biochemical fragmentation and motif identification.

Main Results:

  • LigAlign achieves results consistent with manual annotations for rigid alignments.
  • Flexible alignments by LigAlign produce biochemically reasonable ligand fragmentations.
  • LigAlign successfully identifies conserved structural motifs missed by rigid alignment techniques.

Conclusions:

  • LigAlign offers a significant advancement in analyzing protein-ligand complexes by incorporating ligand flexibility.
  • The system provides a more accurate and comprehensive approach to structural motif identification.
  • LigAlign has the potential to enhance drug discovery and development processes.