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Related Concept Videos

Polymers02:34

Polymers

The word polymer is derived from the Greek words “poly” which means “many” and “mer” which means “parts”. Polymers are long chains of molecules composed of repeating units of smaller molecules, known as monomers. They either occur naturally, such as DNA and proteins, or can be constructed synthetically, like plastics. They have varied structural characteristics, such as linear chains, branched chains, or complex networks, that contribute to the properties that they exhibit. Additionally,...
Polymers02:34

Polymers

The word polymer is derived from the Greek words “poly” which means “many” and “mer” which means “parts”. Polymers are long chains of molecules composed of repeating units of smaller molecules, known as monomers. They either occur naturally, such as DNA and proteins, or can be constructed synthetically, like plastics. They have varied structural characteristics, such as linear chains, branched chains, or complex networks, that contribute to the properties that they exhibit. Additionally,...
Polymers02:34

Polymers

The word polymer is derived from the Greek words “poly” which means “many” and “mer” which means “parts”. Polymers are long chains of molecules composed of repeating units of smaller molecules, known as monomers. They either occur naturally, such as DNA and proteins, or can be constructed synthetically, like plastics. They have varied structural characteristics, such as linear chains, branched chains, or complex networks, that contribute to the properties that they exhibit. Additionally,...
Polymers: Molecular Weight Distribution01:10

Polymers: Molecular Weight Distribution

For any given polymer, the weight average molecular weight (Mw) is higher than, if not equal to, the number average molecular weight (Mn). The only situation in which the weight average molecular weight and the number average molecular weight are equal is when a polymer consists only of chains with equal molecular weight. However, this never happens in a synthetic polymer, since it is difficult to control the polymerization process up to a molecular level with accuracy to a hundred percent.
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...

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On-Chip Octanol-Assisted Liposome Assembly for Bioengineering
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LocalMove: computing on-lattice fits for biopolymers.

Y Ponty1, R Istrate, E Porcelli

  • 1Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

Nucleic Acids Research
|June 17, 2008
PubMed
Summary

LocalMove is a web server that simplifies biomolecule structures into simplified lattice models. It uses advanced algorithms to generate 3D visualizations of protein and RNA conformations.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Protein Data Bank (PDB) files contain essential structural information for proteins and RNA.
  • Representing complex biomolecules in simplified models is crucial for computational analysis.
  • Existing methods may lack efficient on-lattice representation capabilities.

Purpose of the Study:

  • To develop a web server, LocalMove, for generating on-lattice representations of biomolecules.
  • To provide an approximate fit for coarse-grain or backbone models on cubic lattices.
  • To offer a user-friendly tool for visualizing molecular conformations.

Main Methods:

  • Utilizes a Markov Chain Monte-Carlo algorithm with simulated annealing.
  • Computes approximate fits for coarse-grain or backbone models.

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  • Operates on cubic or face-centered cubic lattices.

    • Main Results:

    • LocalMove successfully generates on-lattice representations from input PDB files.
    • The server provides PDB file output and dynamic 3D movies of intermediate conformations.
    • Demonstrates an efficient method for biomolecular structure simplification.

    Conclusions:

    • LocalMove offers a valuable tool for structural bioinformatics research.
    • The web server facilitates the analysis and visualization of protein and RNA structures.
    • Enables efficient exploration of molecular conformations in simplified lattice environments.