ArticleJournal of molecular modeling2023
A semiempirical method optimized for modeling proteins.
Article in Journal of molecular modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
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- Structural Basis for Potent Inhibition of Human DHODH by Quinoline-4-carboxylic Acid Derivatives.ACS omega · 2026Article
- Computer-Based Design to Improve Bacillus thuringiensis Chitinase for Industrial Applications.ChemistryOpen · 2026Article
- Computational chemistry methods based on MNDO and tools for improving their accuracy.Journal of molecular modeling · 2026Article
- A Near Black Box Parameter Optimizer for NDDO-Descendant Semiempirical Methods: Demonstrations for MNDO and AM1.The journal of physical chemistry. A · 2026Article
- Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis.Journal of chemical information and modeling · 2025Article
- SEAMM: A Simulation Environment for Atomistic and Molecular Modeling.The journal of physical chemistry. A · 2025Article
- Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions.Journal of chemical theory and computation · 2025Article
- Prediction of enzyme inhibition (ICJournal of molecular modeling · 2025Article
- Synthesis of Epoxyoxirenes: Phytotoxic Activity and Enzymatic Target Identification.Plants (Basel, Switzerland) · 2025Article
- End-Point Affinity Estimation of Galectin Ligands by Classical and Semiempirical Quantum Mechanical Potentials.Journal of chemical information and modeling · 2025Article
- Geometry-Corrected Quadratic Optimization Algorithm for NDDO-Descendant Semiempirical Models.Journal of chemical theory and computation · 2025Article
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2 authors.
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Abstract
contextIn recent years, semiempirical methods such as PM6, PM6-D3H4, and PM7 have been increasingly used for modeling proteins, in particular enzymes. These methods were designed for more general use, and consequently were not optimized for studying proteins. Because of this, various specific errors have been found that could potentially cast doubt on the validity of these methods for modeling phenomena of biochemical interest such as enzyme catalytic mechanisms and protein-ligand interactions. To correct these and other errors, a new method specifically designed for use in organic and biochemical modeling has been developed.
methodsTwo alterations were made to the procedures used in developing the earlier PMx methods. A minor change was made to the theoretical framework, which affected only the non-quantum theory interatomic interaction function, while the major change involved changing the training set for optimizing parameters, moving the focus to systems of biochemical significance. This involved both the selection of reference data and the weighting factors, i.e., the relative importance that the various data were given. As a result of this change of focus, the accuracy in prediction of heats of formation, hydrogen bonding, and geometric quantities relating to non-covalent interactions in proteins was improved significantly.
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