ArticleJournal of the American Chemical Society2009
Conformational variability of benzamidinium-based inhibitors.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 31 citations in OpenAlex.
- Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.Nature communications · 2024Article
- Improving Small-Molecule Force Field Parameters in Ligand Binding Studies.Frontiers in molecular biosciences · 2021Article
- Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.Nature communications · 2018Article
- Capturing the photo-signaling state of a photoreceptor in a steady-state fashion by binding a transition metal complex.Protein science : a publication of the Protein Society · 2017Article
- Quantum crystallography.Chemical science · 2017Review
- 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
- Automating crystallographic structure solution and refinement of protein-ligand complexes.Acta crystallographica. Section D, Biological crystallography · 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
- QM/MM refinement and analysis of protein bound retinoic acid.Journal of computational chemistry · 2012Article
- Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.Journal of computer-aided molecular design · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Determining the structure of a small molecule bound to a biological receptor (e.g., a protein implicated in a disease state) is a necessary step in structure-based drug design. The preferred conformation of a small molecule can change when bound to a protein, and a detailed knowledge of the preferred conformation(s) of a bound ligand can help in optimizing the affinity of a molecule for its receptor. However, the quality of a protein/ligand complex determined using X-ray crystallography is dependent on the size of the protein, the crystal quality, and the realized resolution. The energy restraints used in traditional X-ray refinement procedures typically use "reduced" (i.e., neglect of electrostatics and dispersion interactions) Engh and Huber force field models that, while quite suitable for modeling proteins, often are less suitable for small molecule structures due to a lack of validated parameters. Through the use of ab initio QM/MM-based X-ray refinement procedures, this shortcoming can be overcome especially in the active site or binding site of a small-molecule inhibitor. Herein, we demonstrate that ab initio QM/MM refinement of an inhibitor/protein complex provides insights into the binding of small molecules beyond what is available using more traditional refinement protocols. In particular, QM/MM refinement studies of benzamidinium derivatives show variable conformational preferences depending on the refinement protocol used and the nature of the active-site region.
Indexed as
Identifiers
What OpenQuestion holds
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.