ArticleJournal of computational chemistry2012
QM/MM refinement and analysis of protein bound retinoic acid.
Article in Journal of computational chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 15 citations in OpenAlex.
- 'International journal of molecular sciences · 2021Article
- Metabolite Structure Assignment Using In Silico NMR Techniques.Analytical chemistry · 2020Article
- Probing biological activity through structural modelling of ligand-receptor interactions of 2,4-disubstituted thiazole retinoids.Bioorganic & medicinal chemistry · 2018Article
- Solving the scalability issue in quantum-based refinement: Q|R#1.Acta crystallographica. Section D, Structural biology · 2017Article
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
- Quantum crystallography.Chemical science · 2017Review
- The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors.MedChemComm · 2017Article
- Q|R: quantum-based refinement.Acta crystallographica. Section D, Structural biology · 2017Article
- Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.International journal of molecular sciences · 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 Retinoic Acids: Effects of Steric Interactions on Nonplanar Conjugated Polyenes.Computational & theoretical chemistry · 2013Article
- Conformational Analysis of Free and Bound Retinoic Acid.Journal of chemical theory and computation · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Retinoic acid (RA) is a vitamin A derivative, which modifies the appearance of fine wrinkles and roughness of facial skin and treats acne and activates gene transcription by binding to heterodimers of the retinoic acid receptor (RAR) and the retinoic X receptor (RXR). There are series of protein bound RA complexes available in the protein databank (PDB), which provides a broad range of information about the different bioactive conformations of RA. To gain further insights into the observed bioactive RA conformations we applied quantum mechanic (QM)/molecular mechanic (MM) approaches to re-refine the available RA protein-ligand complexes. MP2 complete basis set (CBS) extrapolations single energy calculations are also carried out for both the experimental conformations and QM optimized geometries of RA in the gas as well as solution phase. The results demonstrate that the re-refined structures show better geometries for RA than seen in the originally deposited PDB structures through the use of QMs for the ligand in the X-ray refinement procedure. QM/MM re-refined conformations also reduced the computed strain energies found in the deposited crystal conformations for RA. Finally, the dependence of ligand strain on resolution is analyzed. It is shown that ligand strain is not converged in our calculations and is likely an artifact of the typical resolutions employed to study protein-ligand complexes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.