ArticleJournal of chemical theory and computation2007
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy.
Article in Journal of chemical theory and computation, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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Who cites it
99 citing papers in PubMed, 355 citations in OpenAlex.
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- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization.Journal of chemical theory and computation · 2025Article
- High-Resolution Molecular-Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2).Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials.Journal of chemical information and modeling · 2025Article
- Article
- Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of p orbitals.The Journal of chemical physics · 2024Article
- Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2024Article
- Force-field-enhanced neural network interactions: from local equivariant embedding to atom-in-molecule properties and long-range effects.Chemical science · 2023Article
- Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions.Journal of the American Chemical Society · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Fitting Potential Energy Surfaces by Learning the Charge Density Matrix with Permutationally Invariant Polynomials.Journal of chemical theory and computation · 2023Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 2023Article
- Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2023Article
- M-Chem: a Modular Software Package for Molecular Simulation that Spans Scientific Domains.Molecular physics · 2023Article
- Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2022Article
- Non-covalent interactions from a Quantum Chemical Topology perspective.Journal of molecular modeling · 2022Article
- Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles.Journal of computational chemistry · 2022Article
- Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations.Journal of chemical theory and computation · 2022Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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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.