Research graph
References from MPID polarizable force field: GPU implementation and biomolecular simulations. Local targets link to admitted publications; unresolved targets remain external evidence.
Recent advances in polarizable force fields for macromolecules: Microsecond simulations of proteins using the classical Drude oscillator model
10.1021/jz501315h · 2014 · External reference
Classical electrostatics for biomolecular simulations
10.1021/cr300461d · 2014 · External reference
Advanced potential energy surfaces for molecular simulation
10.1021/acs.jpcb.6b06414 · 2016 · External reference
Special issue on polarizable force fields for biomolecular modelling
10.1142/s273741652202001x · 2022 · External reference
CHARMM36m: An improved force field for folded and intrinsically disordered proteins
10.1038/nmeth.4067 · 2017 · External reference
All-atom empirical potential for molecular modeling and dynamics studies of proteins
10.1021/jp973084f · 1998 · External reference
ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
10.1021/acs.jctc.5b00255 · 2015 · External reference
Improved peptide and protein torsional energetics with the OPLS-AA force field
10.1021/acs.jctc.5b00356 · 2015 · External reference
Molecular mechanisms of Na+-driven bile acid transport in human NTCP
10.1016/j.bpj.2024.03.033 · 2024 · External reference
A ‘knob switch’ model for the phosphoregulatory mechanism of KCC3 at the carboxy-terminal domain
10.1021/acs.biochem.4c00523 · 2025 · External reference
Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide
10.1016/j.bpj.2014.06.038 · 2014 · External reference
Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins
10.1073/pnas.1805049115 · 2018 · External reference
Differential impact of the monovalent ions Li+, Na+, K+, and Rb+ on DNA conformational properties
10.1021/jz5024543 · 2015 · External reference
Absolute binding free energies for the SAMPL6 cucurbit [8] uril host-guest challenge via the AMOEBA polarizable force field
10.1007/s10822-018-0147-5 · 2018 · External reference
Current status of the AMOEBA polarizable force field
10.1021/jp910674d · 2010 · External reference
Polarizable atomic multipole-based AMOEBA force field for proteins
10.1021/ct4003702 · 2013 · External reference
Polarizable atomic multipole-based molecular mechanics for organic molecules
10.1021/ct200304d · 2011 · External reference
AMOEBA polarizable atomic multipole force field for nucleic acids
10.1021/acs.jctc.7b01169 · 2018 · External reference
AMOEBA+ classical potential for modeling molecular interactions
10.1021/acs.jctc.9b00261 · 2019 · External reference
An empirical polarizable force field based on the classical Drude oscillator model: Development history and recent applications
10.1021/acs.chemrev.5b00505 · 2016 · External reference
Polarizable force field for peptides and proteins based on the classical Drude oscillator
10.1021/ct400781b · 2013 · External reference
Further optimization and validation of the classical Drude polarizable protein force field
10.1021/acs.jctc.0c00057 · 2020 · External reference
All-atom polarizable force field for DNA based on the classical Drude oscillator model
10.1002/jcc.23611 · 2014 · External reference
A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids
10.1021/jp402860e · 2013 · External reference
Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator
10.1002/bip.22286 · 2013 · External reference
Mapping the Drude polarizable force field onto a multipole and induced dipole model
10.1063/1.4984113 · 2017 · External reference
Unresolved reference
2017 · External reference
Molecular dynamics simulations using the Drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
10.1002/jcc.25339 · 2018 · External reference
Tinker-HP: A massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
10.1039/c7sc04531j · 2018 · External reference
CHARMM at 45: Enhancements in accessibility, functionality, and speed
10.1021/acs.jpcb.4c04100 · 2024 · External reference
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
10.1371/journal.pcbi.1005659 · 2017 · External reference
OpenMM 8: Molecular dynamics simulation with machine learning potentials
10.1021/acs.jpcb.3c06662 · 2023 · External reference
DP/MM: A hybrid model for zinc-protein interactions in molecular dynamics
10.1021/acs.jpclett.3c03158 · 2024 · External reference
Implementation and validation of an OpenMM plugin for the deep potential representation of potential energy
10.3390/ijms25031448 · 2024 · External reference
An empirical extrapolation scheme for efficient treatment of induced dipoles
10.1063/1.4964866 · 2016 · External reference
Molecular polarizabilities calculated with a modified dipole interaction
10.1016/0301-0104(81)85176-2 · 1981 · External reference
Simulating monovalent and divalent ions in aqueous solution using a Drude polarizable force field
10.1021/ct900576a · 2010 · External reference
Representation of ion-protein interactions using the Drude polarizable force-field
10.1021/jp510560k · 2015 · External reference
Direct inversion in the iterative subspace (DIIS) optimization of open-shell, excited-state, and small multiconfiguration SCF wave functions
10.1063/1.449880 · 1986 · External reference
Improved modeling of cation-π and anion-ring interactions using the Drude polarizable empirical force field for proteins
10.1002/jcc.26067 · 2020 · External reference
Structure of ubiquitin refined at 1.8 Å resolution
10.1016/0022-2836(87)90679-6 · 1987 · External reference
Crystal structure of CspA, the major cold shock protein of Escherichia coli
10.1073/pnas.91.11.5119 · 1994 · External reference
Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction
10.1021/jp075531p · 2007 · External reference
Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex
10.1016/j.str.2004.03.017 · 2004 · External reference
Refinement of the structure of recombinant rat intestinal fatty acid-binding apoprotein at 1.2-A resolution
10.1016/s0021-9258(19)50654-8 · 1992 · External reference
Six-site polarizable model of water based on the classical Drude oscillator
10.1063/1.4774577 · 2013 · External reference
A simple polarizable model of water based on classical Drude oscillators
10.1063/1.1598191 · 2003 · External reference
A polarizable model of water for molecular dynamics simulations of biomolecules
10.1016/j.cplett.2005.10.135 · 2006 · External reference
Computationally efficient polarizable md simulations: A simple water model for the classical Drude oscillator polarizable force field
10.1021/acs.jpclett.4c03451 · 2025 · External reference
Revised 4-point water model for the classical Drude oscillator polarizable force field: SWM4-HLJ
10.1021/acs.jctc.4c00966 · 2024 · External reference
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
10.1063/1.464397 · 1993 · External reference
Direct-space corrections enable fast and accurate Lorentz–Berthelot combination rule Lennard–Jones lattice summation
10.1021/acs.jctc.5b00726 · 2015 · External reference
Multiscale dynamics of macromolecules using normal mode Langevin
2010 · External reference
Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
10.1016/j.cplett.2003.12.039 · 2004 · External reference
Algorithms for macromolecular dynamics and constraint dynamics
10.1080/00268977700102571 · 1977 · External reference
CHARMM: The biomolecular simulation program
10.1002/jcc.21287 · 2009 · External reference
Are current molecular dynamics force fields too helical?
10.1529/biophysj.108.132696 · 2008 · External reference
Contact electron-spin coupling of nuclear magnetic moments
10.1063/1.1729860 · 1959 · External reference
Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
10.1021/ja0660406 · 2007 · External reference
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ϕ, ψ and side-chain χ1 and χ2 dihedral angles
10.1021/ct300400x · 2012 · External reference
Determination of ϕ and χ1 angles in proteins from 13C–13C three-bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond?
10.1021/ja970067v · 1997 · External reference
Protein backbone 1H(N)–13Cα and 15N–13Cα residual dipolar and J couplings: New constraints for NMR structure determination
10.1021/ja049049l · 2004 · External reference
Determination of ψ torsion angle restraints from 3 J (Cα, Cα) and 3 J (Cα, HN) coupling constants in proteins
10.1021/ja9928834 · 2000 · External reference
Direct observation of hydrogen bonds in proteins by interresidue 3h J NC′ scalar couplings
10.1021/ja983945d · 1999 · External reference
Correlation between 3h J NC′ and hydrogen bond length in proteins
10.1021/ja9909024 · 1999 · External reference
Structural dependencies of interresidue scalar coupling (h3) J NC′ and donor (1)H chemical shifts in the hydrogen bonding regions of proteins
10.1021/ja012674v · 2002 · External reference
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
10.1002/jcc.23354 · 2013 · External reference
What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis
10.1016/j.jmb.2005.03.001 · 2005 · External reference
Designing a 20-residue protein
10.1038/nsb798 · 2002 · External reference
Conformation of the backbone in unfolded proteins
10.1021/cr040433a · 2006 · External reference
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation
10.1016/j.bpj.2012.07.042 · 2012 · External reference
Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures
10.1038/s42004-021-00537-8 · 2021 · External reference
Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation
10.1021/ja00155a020 · 1995 · External reference
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange
10.1021/bi962018l · 1997 · External reference
Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
10.1021/ja9812610 · 1998 · External reference
Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: Evidence for conformational dynamics in the single-stranded RNA-binding site
10.1021/bi980269j · 1998 · External reference
Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs
10.1038/nsmb.2355 · 2012 · External reference
Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H–15N NMR spectroscopy
10.1021/ja107847d · 2011 · External reference
Signature of mobile hydrogen bonding of lysine side chains from long-range 15N–13C scalar J-couplings and computation
10.1021/ja202219n · 2011 · External reference
Characterization of salt bridges to lysines in the protein G B1 domain
10.1021/ja808223p · 2009 · External reference
How well do force fields capture the strength of salt bridges in proteins?
10.7717/peerj.4967 · 2018 · External reference
Force field development and simulations of intrinsically disordered proteins
10.1016/j.sbi.2017.10.008 · 2018 · External reference
The intrinsic disorder challenge for AlphaFold: A case study of G3BP1 and pathogenic peptide
10.1016/j.isci.2026.115737 · 2026 · External reference
The continuous evolution of biomolecular force fields
10.1016/j.str.2025.05.013 · 2025 · External reference
Phosphorylation drives a dynamic switch in serine/arginine-rich proteins
10.1016/j.str.2013.09.014 · 2013 · External reference
A transferrable range-separated force field for water: Combining the power of both physically-motivated models and machine learning techniques
10.1063/5.0128780 · 2022 · External reference
A fast, convenient, polarizable electrostatic model for molecular dynamics
10.1021/acs.jctc.3c01171 · 2024 · External reference
A simple, polarizable, rigid, 3-point water model using the direct polarization approximation
10.1021/acs.jctc.5c00603 · 2025 · External reference
Induced dipole calculation with E(3)-equivariant neural networks and multipole field perturbation
10.1021/acs.jctc.5c02167 · 2026 · External reference
