XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps Article Swipe
Ajay N. Jain
,
Ann E. Cleves
,
Alexander C. Brueckner
,
Charles A. Lesburg
,
Qiaolin Deng
,
Edward C. Sherer
,
Mikhail Reibarkh
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jmedchem.0c01373
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jmedchem.0c01373
We report a new method for X-ray density ligand fitting and refinement that is suitable for a wide variety of small-molecule ligands, including macrocycles. The approach (called "xGen") augments a force field energy calculation with an electron density fitting restraint that yields an energy reward during the restrained conformational search. The resulting conformer pools balance goodness-of-fit with ligand strain. Real-space refinement from pre-existing ligand coordinates of 150 macrocycles resulted in occupancy-weighted conformational ensembles that exhibited low strain energy. The xGen ensembles improved upon electron density fit compared with the PDB reference coordinates without making use of atom-specific B-factors. Similarly, on nonmacrocycles, de novo fitting produced occupancy-weighted ensembles of many conformers that were generally better-quality density fits than the deposited primary/alternate conformational pairs. The results suggest ubiquitous low-energy ligand conformational ensembles in X-ray diffraction data and provide an alternative to using B-factors as model parameters.
Related Topics
Concepts
Conformational isomerism
Chemistry
Electron density
Ligand (biochemistry)
Conformational ensembles
Crystallography
Protein Data Bank (RCSB PDB)
Atom (system on chip)
Force field (fiction)
Molecule
Computational chemistry
Electron
Molecular dynamics
Stereochemistry
Physics
Artificial intelligence
Computer science
Receptor
Embedded system
Organic chemistry
Biochemistry
Quantum mechanics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.jmedchem.0c01373
- https://pubs.acs.org/doi/pdf/10.1021/acs.jmedchem.0c01373
- OA Status
- hybrid
- Cited By
- 16
- References
- 26
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3082180988
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W3082180988Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1021/acs.jmedchem.0c01373Digital Object Identifier
- Title
-
XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density MapsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2020Year of publication
- Publication date
-
2020-09-02Full publication date if available
- Authors
-
Ajay N. Jain, Ann E. Cleves, Alexander C. Brueckner, Charles A. Lesburg, Qiaolin Deng, Edward C. Sherer, Mikhail ReibarkhList of authors in order
- Landing page
-
https://doi.org/10.1021/acs.jmedchem.0c01373Publisher landing page
- PDF URL
-
https://pubs.acs.org/doi/pdf/10.1021/acs.jmedchem.0c01373Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
-
https://pubs.acs.org/doi/pdf/10.1021/acs.jmedchem.0c01373Direct OA link when available
- Concepts
-
Conformational isomerism, Chemistry, Electron density, Ligand (biochemistry), Conformational ensembles, Crystallography, Protein Data Bank (RCSB PDB), Atom (system on chip), Force field (fiction), Molecule, Computational chemistry, Electron, Molecular dynamics, Stereochemistry, Physics, Artificial intelligence, Computer science, Receptor, Embedded system, Organic chemistry, Biochemistry, Quantum mechanicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
16Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 6, 2024: 2, 2023: 2, 2022: 1, 2021: 5Per-year citation counts (last 5 years)
- References (count)
-
26Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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