ArticleMolecular informatics2011
Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target.
Article in Molecular informatics, 2011. 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.
- Unveiling Interactions between Self-Assembling Peptides and Neuronal Membranes.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Decrypting a Cryptic Allosteric Pocket inCommunications chemistry · 2021Article
- Elucidating the Catalytic Power of Glutamate Racemase by Investigating a Series of Covalent Inhibitors.ChemMedChem · 2018Article
- Article
- In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome.European biophysics journal : EBJ · 2017Article
- Ensemble-based docking: From hit discovery to metabolism and toxicity predictions.Bioorganic & medicinal chemistry · 2016Article
- Article
- Biochemical Characterization of Glutamate Racemase-A New Candidate Drug Target against Burkholderia cenocepacia Infections.PloS one · 2016Article
- Biosynthesis of a Novel Glutamate Racemase Containing a Site-Specific 7-Hydroxycoumarin Amino Acid: Enzyme-Ligand Promiscuity Revealed at the Atomistic Level.ACS central science · 2015Article
- Overcoming dissipation in the calculation of standard binding free energies by ligand extraction.Journal of computational chemistry · 2013Article
- Nexus between protein-ligand affinity rank-ordering, biophysical approaches, and drug discovery.ACS medicinal chemistry letters · 2013Article
- In silico optimization of a fragment-based hit yields biologically active, high-efficiency inhibitors for glutamate racemase.ChemMedChem · 2013Article
- Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations.Journal of chemical information and modeling · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Existing techniques which attempt to predict the affinity of protein-ligand interactions have demonstrated a direct relationship between computational cost and prediction accuracy. We present here the first application of a hybrid ensemble docking and steered molecular dynamics scheme (with a minimized computational cost), which achieves a binding affinity rank-ordering of ligands with a Spearman correlation coefficient of 0.79 and an RMS error of 0.7 kcal/mol. The scheme, termed Flexible Enzyme Receptor Method by Steered Molecular Dynamics (FERM-SMD), is applied to an in-house collection of 17 validated ligands of glutamate racemase. The resulting improved accuracy in affinity prediction allows elucidation of the key structural components of a heretofore unreported glutamate racemase inhibitor (K(i) = 9 µM), a promising new lead in the development of antibacterial therapeutics.
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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.