Research graph
References from Coupling Quantum Mechanical Modeling and Molecular Dynamics on Heterogeneous Supercomputers for Studying Distal Mutation Effects on Drug Binding in HIV-1. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1002/9783527671816
10.1002/9783527671816 · 2013 · External reference
Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity
10.1002/wcms.1574 · 2022 · External reference
Inhomogeneous Electron Gas
10.1103/physrev.136.b864 · 1964 · External reference
Self-Consistent Equations Including Exchange and Correlation Effects
10.1103/physrev.140.a1133 · 1965 · External reference
Shifting sands of hardware and software in exascale quantum mechanical simulations
10.1038/s42254-025-00823-7 · 2025 · External reference
Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance
10.1021/acschembio.9b00370 · 2019 · External reference
Challenges in large scale quantum mechanical calculations
10.1002/wcms.1290 · 2017 · External reference
Design of HIV Protease Inhibitors Targeting Protein Backbone: An Effective Strategy for Combating Drug Resistance
10.1021/ar7001232 · 2008 · External reference
Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope
10.1016/j.jmb.2011.03.053 · 2011 · External reference
Human Immunodeficiency Virus gag and protease: partners in resistance
10.1186/1742-4690-9-63 · 2012 · External reference
CHARMM-GUI: A web-based graphical user interface for CHARMM
10.1002/jcc.20945 · 2008 · External reference
CHARMM: The biomolecular simulation program
10.1002/jcc.21287 · 2009 · External reference
CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
10.1016/j.bpj.2015.11.3431 · 2016 · External reference
Ionization states of the catalytic residues in HIV-1 protease
10.1038/nsb1196-946 · 1996 · External reference
Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site
10.1002/anie.201509989 · 2016 · External reference
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models
10.1021/acs.jpcb.4c02096 · 2024 · External reference
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
10.1038/nmeth.4067 · 2017 · External reference
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
10.1021/ci300363c · 2012 · External reference
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
10.1021/ci3003649 · 2012 · External reference
Comparison of simple potential functions for simulating liquid water
10.1063/1.445869 · 1983 · External reference
Flexibilities of wavelets as a computational basis set for large-scale electronic structure calculations
10.1063/5.0004792 · 2020 · External reference
Accurate and efficient linear scaling DFT calculations with universal applicability
10.1039/c5cp00437c · 2015 · External reference
Generalized Gradient Approximation Made Simple
10.1103/physrevlett.77.3865 · 1996 · External reference
Norm-conserving pseudopotentials with chemical accuracy compared to all-electron calculations
10.1063/1.4793260 · 2013 · External reference
Searching for a Reliable Density Functional for Molecule-Environment Interactions, Found B97M-V/def2-mTZVP
10.1021/acs.jpca.2c02032 · 2022 · External reference
Complexity reduction in density functional theory: Locality in space and energy
10.1063/5.0142652 · 2023 · External reference
Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
10.1021/acs.chemrev.5b00630 · 2016 · External reference
Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis
10.1021/acs.jctc.7b00291 · 2017 · External reference
Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding
10.1021/acs.jctc.9b01152 · 2020 · External reference
Protein-ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors
10.1063/5.0148064 · 2023 · External reference
Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling
10.1098/rsif.2023.0614 · 2024 · External reference
Pair interaction energy decomposition analysis
10.1002/jcc.20496 · 2007 · External reference
10.1007/978-1-0716-0282-9
10.1007/978-1-0716-0282-9 · 2020 · External reference
FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method
10.1021/acs.jcim.0c01062 · 2021 · External reference
FMO-guided design of darunavir analogs as HIV-1 protease inhibitors
10.1038/s41598-024-53940-1 · 2024 · External reference
Unresolved reference
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Unresolved reference
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Unresolved reference
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10.1145/3784828.3785259
10.1145/3784828.3785259 · External reference
Exploratory data science on supercomputers for quantum mechanical calculations
10.1088/2516-1075/ad4b80 · 2024 · External reference
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
10.1002/jcc.21787 · 2011 · External reference
Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance
10.1128/jvi.02531-09 · 2010 · External reference
Enhanced sampling in molecular dynamics
10.1063/1.5109531 · 2019 · External reference
Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional
10.1039/d1cp00206f · 2021 · External reference
10.1002/9783527671816
10.1002/9783527671816 · ExternalCitation · doi-reference
Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site
10.1002/anie.201509989 · ExternalCitation · doi-reference
Pair interaction energy decomposition analysis
10.1002/jcc.20496 · ExternalCitation · doi-reference
CHARMM-GUI: A web-based graphical user interface for CHARMM
10.1002/jcc.20945 · ExternalCitation · doi-reference
CHARMM: The biomolecular simulation program
10.1002/jcc.21287 · ExternalCitation · doi-reference
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
10.1002/jcc.21787 · ExternalCitation · doi-reference
Challenges in large scale quantum mechanical calculations
10.1002/wcms.1290 · ExternalCitation · doi-reference
Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity
10.1002/wcms.1574 · ExternalCitation · doi-reference
10.1007/978-1-0716-0282-9
10.1007/978-1-0716-0282-9 · ExternalCitation · doi-reference
CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
10.1016/j.bpj.2015.11.3431 · ExternalCitation · doi-reference
Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope
10.1016/j.jmb.2011.03.053 · ExternalCitation · doi-reference
Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
10.1021/acs.chemrev.5b00630 · ExternalCitation · doi-reference
FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method
10.1021/acs.jcim.0c01062 · ExternalCitation · doi-reference
Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis
10.1021/acs.jctc.7b00291 · ExternalCitation · doi-reference
Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding
10.1021/acs.jctc.9b01152 · ExternalCitation · doi-reference
Searching for a Reliable Density Functional for Molecule-Environment Interactions, Found B97M-V/def2-mTZVP
10.1021/acs.jpca.2c02032 · ExternalCitation · doi-reference
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models
10.1021/acs.jpcb.4c02096 · ExternalCitation · doi-reference
Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance
10.1021/acschembio.9b00370 · ExternalCitation · doi-reference
Design of HIV Protease Inhibitors Targeting Protein Backbone: An Effective Strategy for Combating Drug Resistance
10.1021/ar7001232 · ExternalCitation · doi-reference
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
10.1021/ci300363c · ExternalCitation · doi-reference
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
10.1021/ci3003649 · ExternalCitation · doi-reference
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
10.1038/nmeth.4067 · ExternalCitation · doi-reference
Ionization states of the catalytic residues in HIV-1 protease
10.1038/nsb1196-946 · ExternalCitation · doi-reference
FMO-guided design of darunavir analogs as HIV-1 protease inhibitors
10.1038/s41598-024-53940-1 · ExternalCitation · doi-reference
Shifting sands of hardware and software in exascale quantum mechanical simulations
10.1038/s42254-025-00823-7 · ExternalCitation · doi-reference
Accurate and efficient linear scaling DFT calculations with universal applicability
10.1039/c5cp00437c · ExternalCitation · doi-reference
Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional
10.1039/d1cp00206f · ExternalCitation · doi-reference
Comparison of simple potential functions for simulating liquid water
10.1063/1.445869 · ExternalCitation · doi-reference
Norm-conserving pseudopotentials with chemical accuracy compared to all-electron calculations
10.1063/1.4793260 · ExternalCitation · doi-reference
Enhanced sampling in molecular dynamics
10.1063/1.5109531 · ExternalCitation · doi-reference
Flexibilities of wavelets as a computational basis set for large-scale electronic structure calculations
10.1063/5.0004792 · ExternalCitation · doi-reference
Complexity reduction in density functional theory: Locality in space and energy
10.1063/5.0142652 · ExternalCitation · doi-reference
Protein-ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors
10.1063/5.0148064 · ExternalCitation · doi-reference
Exploratory data science on supercomputers for quantum mechanical calculations
10.1088/2516-1075/ad4b80 · ExternalCitation · doi-reference
Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling
10.1098/rsif.2023.0614 · ExternalCitation · doi-reference
Inhomogeneous Electron Gas
10.1103/physrev.136.b864 · ExternalCitation · doi-reference
Self-Consistent Equations Including Exchange and Correlation Effects
10.1103/physrev.140.a1133 · ExternalCitation · doi-reference
Generalized Gradient Approximation Made Simple
10.1103/physrevlett.77.3865 · ExternalCitation · doi-reference
Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance
10.1128/jvi.02531-09 · ExternalCitation · doi-reference
10.1145/3784828.3785259
10.1145/3784828.3785259 · ExternalCitation · doi-reference
Human Immunodeficiency Virus gag and protease: partners in resistance
10.1186/1742-4690-9-63 · ExternalCitation · doi-reference
