ArticleActa crystallographica. Section D, Biological crystallography2012
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 23 citations in OpenAlex.
- Ubiquitin-specific protease 7 inhibitors reveal a differentiated mechanism of p53-driven anti-cancer activity.iScience · 2024Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- Validation of ligands in macromolecular structures determined by X-ray crystallography.Acta crystallographica. Section D, Structural biology · 2018Article
- Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.Protein science : a publication of the Protein Society · 2018Article
- Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.Acta crystallographica. Section D, Structural biology · 2016Article
- Protein-ligand cocrystal structures: we can do better.ACS medicinal chemistry letters · 2014Article
- Structure of the Arabidopsis thaliana TOP2 oligopeptidase.Acta crystallographica. Section F, Structural biology communications · 2014Article
- Article
- Automating crystallographic structure solution and refinement of protein-ligand complexes.Acta crystallographica. Section D, Biological crystallography · 2014Article
- OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION.Journal of theoretical & computational chemistry · 2013Article
- Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program.Journal of chemical theory and computation · 2013Article
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3 authors at 1 institution in 1 country.
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Abstract
All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.
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