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Related Concept Videos

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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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

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VSEPR Theory for Determination of Electron Pair Geometries

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Related Experiment Video

Updated: May 7, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Cross-link guided molecular modeling with ROSETTA.

Abdullah Kahraman1, Franz Herzog, Alexander Leitner

  • 1Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.

Plos One
|September 27, 2013
PubMed
Summary
This summary is machine-generated.

Chemical cross-linking mass spectrometry provides distance restraints for protein structures. New workflows and a database (XLdb) improve integration into molecular modeling, enhancing structural analysis of protein complexes.

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Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Chemical cross-linking followed by mass spectrometry (CX-MS) yields distance restraints for low-resolution protein structures.
  • Mature CX-MS technology necessitates advanced methods for integrating distance restraints into molecular modeling.

Purpose of the Study:

  • To introduce novel workflows for integrating CX-MS data into ROSETTA for protein modeling and docking.
  • To present XLdb, a comprehensive database of chemical cross-links.
  • To evaluate the impact of cross-links on protein docking accuracy.

Main Methods:

  • Development of three ROSETTA-based workflows for incorporating CX-MS distance restraints.
  • Utilizing Xwalk software for cross-link data validation and visualization.
  • Compiling and mapping cross-links in the XLdb database to Protein Data Bank structures.
  • Assessing the effect of virtual cross-links on protein-protein docking using a reference dataset.

Main Results:

  • Successful integration of CX-MS data into ROSETTA modeling and docking protocols.
  • Xwalk facilitates efficient cross-link data integration.
  • XLdb contains 506 intra-protein and 62 inter-protein cross-links from 14 publications.
  • Inter-protein cross-links reduced protein docking prediction RMSD by an average of 5.0 Å.

Conclusions:

  • The presented workflows and XLdb provide effective guidelines for integrating CX-MS data into molecular modeling.
  • These advancements will facilitate the structural analysis of large and transient protein complexes using hybrid methods.