ArticleJournal of chemical theory and computation2013
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 269 papers.
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269 citing papers in PubMed.
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- Quantum Chemistry Calculations of Circularly Polarized Luminescence (CPL): From Spectral Modeling to Molecular Design.Chemical reviews · 2025Review
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- Elucidation of the Catalytic Apparatus and Mechanism of Human Chitotriosidase‑1.ACS catalysis · 2025Article
209 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and
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