ReviewInternational journal of molecular sciences2016
Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.
Review in International journal of molecular sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed, 35 citations in OpenAlex.
- Computational discovery of AKT serine/threonine kinase 1 inhibitors through shape screening for rheumatoid arthritis intervention.Molecular diversity · 2025Article
- Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions.The journal of physical chemistry. B · 2024Article
- HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham.Frontiers in molecular biosciences · 2023Review
- Machine learning classification can reduce false positives in structure-based virtual screening.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A.Chemical science · 2019Article
- Article
- Disease-associated missense mutations in GluN2B subunit alter NMDA receptor ligand binding and ion channel properties.Nature communications · 2018Article
- Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.Advances in bioinformatics · 2017Article
- A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1.Journal of molecular modeling · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We review the first successes and failures of a "new wave" of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of "enhanced", dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.
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.