Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Organization01:24

Protein Organization

9.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
9.0K
Gene Families01:57

Gene Families

9.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.8K
Protein and Protein Structure02:15

Protein and Protein Structure

86.6K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
86.6K
X-ray Crystallography02:18

X-ray Crystallography

25.7K
The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
25.7K
Protein Folding01:22

Protein Folding

125.9K
Overview
125.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Report of high data rate macromolecular crystallography (HDRMX) meeting, 23 July 2025.

Structural dynamics (Melville, N.Y.)·2026
Same author

Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.

Nature communications·2026
Same author

Mapping the avoid-ome: a systematic open-science approach to predictive ADMET.

Nature communications·2026
Same author

Inhibiting the interaction between the mitochondrial receptor Tom70 and SARS CoV 2 Orf9b with small molecules.

bioRxiv : the preprint server for biology·2026
Same author

Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA.

bioRxiv : the preprint server for biology·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jan 10, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

10.3K

Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data.

Matthew Hancock1, James Holton2,3,4, James S Fraser1

  • 1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.

Biorxiv : the Preprint Server for Biology
|November 24, 2025
PubMed
Summary

MultiXray software models protein conformations using multiple X-ray datasets and a force field. This Bayesian approach improves atomic structure accuracy by capturing diverse protein states under various experimental conditions.

More Related Videos

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.5K
Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin
11:17

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Published on: March 10, 2021

6.8K

Related Experiment Videos

Last Updated: Jan 10, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

10.3K
Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.5K
Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin
11:17

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Published on: March 10, 2021

6.8K

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein atomic structure is determined from crystal X-ray diffraction patterns.
  • Crystallography typically yields a single atomic model, but proteins exist in multiple conformational states.
  • A single model may not fully represent the protein's dynamic nature and X-ray data.

Purpose of the Study:

  • To develop and validate MultiXray, a Bayesian method for multi-state, multi-condition modeling in X-ray crystallography.
  • To improve protein structure accuracy by integrating multiple X-ray datasets collected under different experimental conditions.
  • To address the challenge of lower data-to-parameter ratios in multi-state modeling.

Main Methods:

  • MultiXray utilizes multiple X-ray datasets and a molecular mechanics force field as input.
  • It models multiple protein conformational states and their respective weights under each condition.
  • Bayesian posterior model density and biased molecular dynamics simulations are employed for model generation and refinement.

Main Results:

  • Benchmarking on simulated CypA data showed improved R-free from 0.105 to 0.089 with a second X-ray dataset.
  • Application to SARS-CoV-2 Mpro temperature-dependent data improved R-free from 0.253 to 0.237.
  • The method successfully integrates diverse experimental data to refine structural models.

Conclusions:

  • MultiXray enhances protein structure modeling accuracy by incorporating multiple conformational states and experimental conditions.
  • The integration of multiple X-ray datasets significantly improves model quality.
  • MultiXray is implemented in open-source Integrative Modeling Platform (IMP) software, compatible with Phenix, facilitating broader application.