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X-ray Crystallography

X-ray Crystallography

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.
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$X-ray Diffraction of Biological Samples$ 01:10

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Related Experiment Video

Updated: Nov 24, 2025

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.

Jeffrey Mendenhall¹, Benjamin P Brown², Sandeepkumar Kothiwale¹

¹Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 United States.

Journal of Chemical Information and Modeling

|December 22, 2020

Summary

This summary is machine-generated.

The improved BioChemical Library (BCL)::Conf algorithm now uses a rotamer library from the Crystallography Open Database (COD), outperforming existing methods in protein-ligand binding conformer recovery.

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Area of Science:

Computational Chemistry
Cheminformatics
Structural Biology

Background:

The BioChemical Library (BCL)::Conf algorithm previously used a Cambridge Structural Database (CSD) derived rotamer library.
Advancements in computational chemistry necessitate improved conformer generation algorithms.

Purpose of the Study:

To enhance the BCL::Conf algorithm with a new rotamer library.
To evaluate the performance of the improved BCL::Conf against state-of-the-art conformer generators.

Main Methods:

Transitioned BCL::Conf to utilize a rotamer library derived from the Crystallography Open Database (COD).
Assessed performance on native conformer recovery using the Platinum dataset of protein-ligand complexes.
Compared results against over a dozen established conformer generation algorithms.

Main Results:

The improved BCL::Conf significantly outperforms the CSD conformer generation algorithm in binding conformer recovery.
Achieved high performance across various ensemble sizes with comparable generation rates.
The new BCL::Conf utilizes a license-free COD-derived rotamer library.

Conclusions:

The enhanced BCL::Conf algorithm offers superior performance for protein-ligand binding conformer generation.
The transition to a COD-derived library makes BCL::Conf more accessible for academic research.
BCL::Conf is freely available for academic use and accessible via a webserver.