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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Digestion01:02

Protein Digestion

Protein digestion begins in the stomach, where the highly acidic environment can easily disrupt protein structure by exposing the peptide bonds of polypeptide chains. After polypeptide chains are broken into individual amino acids by a series of digestive enzymes, the amino acids are transported to the liver via the bloodstream to produce energy.
Peptidoglycan Synthesis01:28

Peptidoglycan Synthesis

Structure of PeptidoglycanPeptidoglycan is a vital structural component of the bacterial cell wall, providing mechanical strength and shape to the cell. It consists of repeating units of two sugars—N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)—linked by β-1,4 glycosidic bonds. These sugar chains are cross-linked by short peptide chains, forming a mesh-like polymer that surrounds the bacterial plasma membrane.Cytoplasmic Phase – Precursor SynthesisPeptidoglycan biosynthesis begins in...

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Related Experiment Video

Updated: May 11, 2026

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
13:37

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Published on: June 20, 2014

PeptideBuilder: A simple Python library to generate model peptides.

Matthew Z Tien1, Dariya K Sydykova, Austin G Meyer

  • 1Department of Biochemistry & Molecular Biology, The University of Chicago , Chicago, IL , USA.

Peerj
|May 30, 2013
PubMed
Summary
This summary is machine-generated.

This Python library simplifies creating polypeptide models with specific backbone angles. It allows users to easily generate peptide structures in desired conformations using Python code.

Keywords:
Computational biologyModel peptidesMolecular modelingProtein structure

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Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
13:37

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Published on: June 20, 2014

Solid-phase Submonomer Synthesis of Peptoid Polymers and their Self-Assembly into Highly-Ordered Nanosheets
13:42

Solid-phase Submonomer Synthesis of Peptoid Polymers and their Self-Assembly into Highly-Ordered Nanosheets

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Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Accurate modeling of polypeptide structures is crucial for understanding protein function and designing novel therapeutics.
  • Generating custom peptide models with specific conformations can be challenging with existing tools.

Purpose of the Study:

  • To introduce a user-friendly Python library for constructing polypeptide models from scratch.
  • To enable the generation of peptide models with pre-specified backbone angles and conformations.

Main Methods:

  • The library provides a simple Python interface for adding amino acid residues to a peptide chain.
  • Users can specify desired backbone angles and conformations for the generated peptide models.
  • Default values for bond angles and lengths are provided, with options for manipulation.

Main Results:

  • The library facilitates the rapid generation of custom polypeptide models.
  • It allows for precise control over peptide backbone conformation through Python scripting.
  • The tool is designed for ease of use, requiring minimal code for model construction.

Conclusions:

  • This Python library offers a straightforward approach to building custom peptide models.
  • It serves as a valuable tool for researchers needing to generate specific peptide conformations for further analysis.
  • The library complements existing tools for energy minimization and rotamer packing.