ArticleProtein science : a publication of the Protein Society2006
Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method.Journal of chemical theory and computation · 2020Article
- Solving the scalability issue in quantum-based refinement: Q|R#1.Acta crystallographica. Section D, Structural biology · 2017Article
- Quantum crystallography.Chemical science · 2017Review
- Q|R: quantum-based refinement.Acta crystallographica. Section D, Structural biology · 2017Article
- Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.Biochemical Society transactions · 2016Review
- Using quantum mechanical approaches to study biological systems.Accounts of chemical research · 2014Article
- Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.Journal of chemical theory and computation · 2013Article
- Conformational Analysis of Free and Bound Retinoic Acid.Journal of chemical theory and computation · 2012Article
- PDB ligand conformational energies calculated quantum-mechanically.Journal of chemical information and modeling · 2012Article
- Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method.The journal of physical chemistry. B · 2012Article
- QM/MM refinement and analysis of protein bound retinoic acid.Journal of computational chemistry · 2012Article
- Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.Journal of computer-aided molecular design · 2011Article
- Trends in template/fragment-free protein structure prediction.Theoretical chemistry accounts · 2011Article
- QM/MM X-ray refinement of zinc metalloenzymes.Journal of inorganic biochemistry · 2010Article
- Application of the PM6 method to modeling proteins.Journal of molecular modeling · 2009Article
- Conformational variability of benzamidinium-based inhibitors.Journal of the American Chemical Society · 2009Article
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5 authors.
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Abstract
A critical evaluation of the performance of X-ray refinement protocols using various energy functions is presented using the bovine pancreatic trypsin inhibitor (BPTI) protein. The four potential energy functions we explored include: (1) fully quantum mechanical calculations; (2) one based on an incomplete molecular mechanics (MM) energy function employed in the Crystallography and NMR System (CNS) with empirical parameters developed by Engh and Huber (EH), which lacks electrostatic and attractive van der Waals terms; (3) one based on a complete MM energy function (AMBER ff99 parameter set); and (4) the same as 3, with the addition of a Generalized Born (GB) implicit solvation term. The R, R (free), real space R values of the refined structures and deviations from the original experimental structure were used to assess the relative performance. It was found that at 1 Angstrom resolution the physically based energy functions 1, 3, and 4 performed better than energy function 2, which we attribute to the better representation of key interactions, particularly electrostatics. The observed departures from the experimental structure were similar for the refinements with physically based energy functions and were smaller than the structure refined with EH. A test refinement was also performed with the reflections truncated at a high-resolution cutoff of 2.5 Angstrom and with random perturbations introduced into the initial coordinates, which showed that low-resolution refinements with physically based energy functions held the structure closer to the experimental structure solved at 1 Angstrom resolution than the EH-based refinements.
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