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

Determination of Crystal Structures01:29

Determination of Crystal Structures

138
In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
138
X-ray Crystallography02:18

X-ray Crystallography

21.6K
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...
21.6K

You might also read

Related Articles

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

Sort by
Same author

The Critical Period Microbiota Shape Brain Plasticity.

bioRxiv : the preprint server for biology·2026
Same author

Evaluating the Intelligence of large language models: A comparative study using verbal and visual IQ tests.

Computers in human behavior. Artificial humans·2026
Same author

The nBAF complex subunit CREST/SS18L1 regulates hippocampal memory processes via tyrosine 397 and histone acetyltransferase CBP.

Cell reports·2026
Same author

Circadian reprogramming by timed sodium intake reveals transcriptional pathways of daily salt handling in the colon.

Science advances·2026
Same author

Chronic intermittent hypoxia reshapes circadian metabolic architecture in a model of sleep apnea.

Science advances·2026
Same author

A Dataset of Plausible Proton Transfer Steps for Arrow-Pushing Mechanisms.

Scientific data·2026
Same journal

Correction to "AstraMEV (AI-Guided Structural Assembly of Multi-Epitope Vaccines) Against Infectious Bronchitis Virus".

Journal of chemical information and modeling·2026
Same journal

MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations.

Journal of chemical information and modeling·2026
Same journal

Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.

Journal of chemical information and modeling·2026
Same journal

Structural and Thermodynamic Discrimination between Agonists and Antagonists of Retinoic Acid Receptor γ and the Vitamin D Receptor.

Journal of chemical information and modeling·2026
Same journal

PACEff Builder: An Efficient Platform for Constructing PACE Hybrid-Resolution Models for Molecular Dynamics Simulations of Aqueous Protein, Peptide Assembly, and Membrane Protein Systems.

Journal of chemical information and modeling·2026
Same journal

TransKla: A Local-Global Cross-Attention Based Transformer Approach for Prediction of Lysine Lactylation Sites.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: May 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.1K

Small-molecule 3D structure prediction using open crystallography data.

Peter Sadowski1, Pierre Baldi

  • 1Institute for Genomics and Bioinformatics , University of California, Irvine , Irvine, California 92697, United States.

Journal of Chemical Information and Modeling
|November 23, 2013
PubMed
Summary
This summary is machine-generated.

A new COSMOS algorithm predicts small molecule 3D structures with improved accuracy and speed. This free tool, using an open data library, outperforms existing methods, making advanced chemoinformatics accessible.

More Related Videos

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

9.4K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K

Related Experiment Videos

Last Updated: May 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.1K
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

9.4K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K

Area of Science:

  • Chemoinformatics
  • Computational Chemistry
  • Structural Biology

Background:

  • Predicting 3D molecular structures is crucial but challenging, with significant accuracy disparities between proprietary and free algorithms.
  • The previous COSMOS algorithm showed promise but was limited by its reliance on the proprietary Cambridge Structural Database.
  • A need exists for accurate, accessible, and efficient tools for small molecule 3D structure prediction.

Purpose of the Study:

  • To present an updated, freely available version of the COSMOS structure prediction algorithm.
  • To introduce a new COSMOS structure library derived from open data sources.
  • To evaluate the performance of the enhanced COSMOS predictor against existing free methods.

Main Methods:

  • Development of an updated COSMOS algorithm incorporating a novel structure library sourced from open data.
  • Benchmarking COSMOS against freely available structure prediction tools, such as Open Babel.
  • Performance evaluation based on root-mean-square deviation (RMSD) and prediction time.

Main Results:

  • The updated COSMOS predictor achieved mean RMSDs of 1.16 Å for organic and 1.68 Å for metal-organic structures.
  • COSMOS demonstrated a 17% and 20% reduction in RMSD compared to Open Babel for respective structure types.
  • The algorithm achieved a mean prediction time of 60 ms per molecule, significantly outperforming Open Babel in speed.

Conclusions:

  • The enhanced COSMOS algorithm offers a significant improvement in accuracy and speed for small molecule 3D structure prediction.
  • Its reliance on open data and free availability democratizes access to advanced chemoinformatics tools.
  • The ChemDB Web portal provides accessible resources, including a web server and downloadable software, for utilizing COSMOS.