Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein–Ligand Binding Affinities Dominated by Cation−π Interactions

Repurposing Existing Molecular Machines through Accurate Regulation of Cooperative Motions

(2021) Haohao Fu et al.   Journal of Physical Chemistry Letters

BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations

(2021) Haohao Fu et al.   Journal of Chemical Information and Modeling

Cation-π interactions and their functional roles in membrane proteins

(2021) Daniel T Infield et al.   JOURNAL OF MOLECULAR BIOLOGY

Nanomachine-Assisted Ion Transport Across Membranes: From Mechanism to Rational Design and Applications

(2021) Hong Zhang et al.   Journal of Physical Chemistry Letters

Polarisable force fields: what do they add in biomolecular simulations?

(2020) VS Sandeep Inakollu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Efficient Estimation of Absolute Binding Free Energy for a Homeodomain–DNA Complex from Nonequilibrium Pulling Simulations

(2020) David Jakubec et al.   Journal of Chemical Theory and Computation

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

Capturing Protein–Ligand Recognition Pathways in Coarse-Grained Simulation

(2020) Bhupendra R. Dandekar et al.   Journal of Physical Chemistry Letters

Accurate Description of Cation−π Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost

(2020) Han Liu et al.   Journal of Chemical Theory and Computation

Explicit Representation of Cation−π Interactions in Force Fields with 1/r4 Nonbonded Terms

(2020) Aysegul Turupcu et al.   Journal of Chemical Theory and Computation

Ligand binding free-energy calculations with funnel metadynamics

(2020) Stefano Raniolo et al.   Nature Protocols

GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions

(2019) Christoph Bannwarth et al.   Journal of Chemical Theory and Computation

Improved Modeling of Cation‐π and Anion‐Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins

(2019) Fang‐Yu Lin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases

(2019) Zhiyou Zong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Taming Rugged Free Energy Landscapes Using an Average Force

(2019) Haohao Fu et al.   ACCOUNTS OF CHEMICAL RESEARCH

String Method for Protein–Protein Binding Free-Energy Calculations

(2019) Donghyuk Suh et al.   Journal of Chemical Theory and Computation

Standard Binding Free Energy of a SIM–SUMO Complex

(2019) Alex Kötter et al.   Journal of Chemical Theory and Computation

Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains

(2019) Esam A. Orabi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Combining Free Energy Simulations and NMR Chemical-Shift Perturbation To Identify Transient Cation−π Contacts in Proteins

(2019) André A. O. Reis et al.   Journal of Chemical Information and Modeling

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations

(2018) Haohao Fu et al.   Journal of Chemical Information and Modeling

Cation−π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

(2018) Esam A. Orabi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

NAMD goes quantum: an integrative suite for hybrid simulations

(2018) Marcelo C R Melo et al.   NATURE METHODS

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys

(2018) Haohao Fu et al.   Journal of Physical Chemistry Letters

Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field

(2018) Hanif M. Khan et al.   Journal of Chemical Theory and Computation

Curvature of Buckybowl Corannulene Enhances Its Binding to Proteins

(2018) Shuangli Du et al.   Journal of Physical Chemistry C

Simulating the Chelate Effect

(2018) Arkajyoti Sengupta et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

ISA-Pol: distributed polarizabilities and dispersion models from a basis-space implementation of the iterated stockholder atoms procedure

(2018) Alston J. Misquitta et al.   THEORETICAL CHEMISTRY ACCOUNTS

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

(2017) Haohao Fu et al.   Journal of Chemical Theory and Computation

A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86)

(2017) Stefan Grimme et al.   Journal of Chemical Theory and Computation

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Polarizable force field development for lipids and their efficient applications in membrane proteins

(2017) Huiying Chu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Improving the Force Field Description of Tyrosine–Choline Cation−π Interactions: QM Investigation of Phenol–N(Me)4+ Interactions

(2016) Hanif M. Khan et al.   Journal of Chemical Theory and Computation

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations

(2016) Haohao Fu et al.   Journal of Chemical Theory and Computation

Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

(2016) Adrien Lesage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Chemically Programmed Proximal Ligand Enhances the Catalytic Properties of a Heme Enzyme

(2016) Anthony P. Green et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia

(2016) S. Picaud et al.   Science Advances

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses

(2015) Ariane Hammitzsch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

(2014) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Molecular Dynamics of β-Hairpin Models of Epigenetic Recognition Motifs

(2012) Xiange Zheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Recognition at the Active Site of Factor Xa: Cation-π Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water

(2011) Laura M. Salonen et al.   CHEMISTRY-A EUROPEAN JOURNAL

Cation−π and π–π Interactions in Aqueous Solution Studied Using Polarizable Potential Models

(2011) Esam A. Orabi et al.   Journal of Chemical Theory and Computation

Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions

(2009) Fabien Archambault et al.   Journal of Chemical Theory and Computation

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes

(2009) Scott P. Brown et al.   JOURNAL OF MEDICINAL CHEMISTRY