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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...
Polymer Classification: Stereospecificity01:26

Polymer Classification: Stereospecificity

Polymerization generates chiral centers along the entire backbone of a polymer chain. Accordingly, the stereochemistry of the substituent group has a significant effect on polymer properties. Polymers formed from monosubstituted alkene monomers feature chiral carbons at every alternate position in the polymer backbone. Relative to the predominant orientation of substituents at the adjacent chiral carbons, the polymer can exist in three different configurations: isotactic, syndiotactic, and...
Polymer Classification: Architecture01:14

Polymer Classification: Architecture

Polymers are classified as linear or branched on the basis of their chain architecture. The polymer chains in linear polymers have a long chain-like structure with minimal to no branching at all. Even if a polymer features large substituent groups on the monomer, which appear as branches to the skeleton, it is not considered a branched polymer. A branched polymer contains secondary polymer chains that arise from the main polymer chain. The branching occurs when the polymer growth shifts from...

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An Open-Source Framework for Mass Calculation of Antibody-Based Therapeutic Molecules
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Published on: June 16, 2023

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

Noel M O'Boyle1, Chris Morley, Geoffrey R Hutchison

  • 1Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK. baoilleach@gmail.com

Chemistry Central Journal
|March 11, 2008
PubMed
Summary

Pybel is a Python module providing access to the OpenBabel cheminformatics toolkit. It simplifies common tasks like data analysis and file parsing for Python programmers, enhancing chemical information manipulation.

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Area of Science:

  • Computational Chemistry
  • Cheminformatics

Background:

  • Python is ideal for cheminformatics tasks like data analysis.
  • Cheminformatics toolkits are often in C++ for efficiency.
  • Pybel bridges Python and the OpenBabel toolkit.

Purpose of the Study:

  • To provide Python access to the OpenBabel toolkit.
  • To simplify common cheminformatics tasks for Python users.

Main Methods:

  • Pybel wraps OpenBabel toolkit bindings.
  • Utilizes Python iterators for simplified looping.
  • Allows interconversion between Pybel Molecule and OpenBabel OBMol objects.

Main Results:

  • Simplifies reading/writing molecular files and calculating fingerprints.
  • Enhances efficiency in processing molecular data.
  • Enables access to all OpenBabel methods via interconversion.

Conclusions:

  • Pybel enables rapid development of Python scripts for chemical information manipulation.
  • It is open-source and cross-platform.
  • Offers the power of OpenBabel to Python programmers.