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Conserved Binding Sites

Conserved Binding Sites

Conserved Binding Sites

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...

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding Sites

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 Linkage

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

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cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization.

Tom A Young¹, Razvan Gheorghe¹, Fernanda Duarte¹

¹Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.

Journal of Chemical Information and Modeling

|June 25, 2020

Summary

This summary is machine-generated.

A new computational toolkit, cgbind, enables rapid design and property prediction for functional metallocages. This accelerates the discovery of novel catalysts and substrate hosts through high-throughput virtual screening.

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Area of Science:

Supramolecular Chemistry
Computational Chemistry
Materials Science

Background:

Metallocages represent a vast, underexplored area of chemical space for catalysis and host-guest chemistry.
Tailoring metallocage structures for specific applications remains a significant challenge in supramolecular chemistry.

Purpose of the Study:

To introduce cgbind, an open-source computational toolkit for the construction, characterization, and property prediction of functional metallocages.
To demonstrate the toolkit's capability in accelerating the design and screening of novel supramolecular structures.

Main Methods:

Utilizing known structural scaffolds and computationally efficient methods for property evaluation.
Employing cgbind for library construction, accurate geometry generation, and substrate binding prediction.
Benchmarking against experimental crystal structures and semiempirical quantum mechanics methods.

Main Results:

Demonstrated ability to construct diverse metallocage libraries with varied topologies and linker functionalities.
Achieved accurate geometry generation with RMSD < 1.5 Å compared to crystal structures.
Predicted substrate binding with accuracy comparable to semiempirical QM methods, achieving results in seconds.

Conclusions:

cgbind facilitates the rapid design and characterization of functional metallocages.
The toolkit enables high-throughput virtual screening, accelerating the discovery of new hosts and catalysts.
Open-source availability and a web-based GUI enhance accessibility for researchers.