Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method

M. Rami Reddy; Mark D. Erion

doi:10.1021/ja072905j

Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method

Journal of the American Chemical Society ◽

10.1021/ja072905j ◽

2007 ◽

Vol 129 (30) ◽

pp. 9296-9297 ◽

Cited By ~ 27

Author(s):

M. Rami Reddy ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation

Download Full-text

Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method

Journal of Computational Chemistry ◽

10.1002/jcc.20617 ◽

2007 ◽

Vol 28 (5) ◽

pp. 932-937 ◽

Cited By ~ 8

Author(s):

Ravichandra Mutyala ◽

R. N. Reddy ◽

M. Sumakanth ◽

P. Reddanna ◽

M. Rami Reddy

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Adenosine Monophosphate ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation

Download Full-text

Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.8b00826 ◽

2018 ◽

Vol 15 (1) ◽

pp. 424-435 ◽

Cited By ~ 13

Author(s):

César de Oliveira ◽

Haoyu S. Yu ◽

Wei Chen ◽

Robert Abel ◽

Lingle Wang

Keyword(s):

Free Energy ◽

Free Energy Perturbation ◽

Perturbation Approach ◽

Binding Affinities ◽

Relative Binding ◽

Energy Perturbation

Download Full-text

Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies

Journal of Computational Chemistry ◽

10.1002/jcc.20510 ◽

2006 ◽

Vol 28 (2) ◽

pp. 491-494 ◽

Cited By ~ 24

Author(s):

M. Rami Reddy ◽

U. C. Singh ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Ab Initio ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

Download Full-text

Calculation of the relative binding free energy of three inhibitors of the photosynthetic reaction center of Rhodopseudomonas viridis using the molecular dynamics/free energy perturbation method

Journal of the American Chemical Society ◽

10.1021/ja00038a046 ◽

1992 ◽

Vol 114 (12) ◽

pp. 4762-4769 ◽

Cited By ~ 1

Author(s):

John E. Mertz ◽

Jan W. Andzelm ◽

Detlef Labrenz ◽

Ursula Egner

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Perturbation Method ◽

Reaction Center ◽

Binding Free Energy ◽

Photosynthetic Reaction Center ◽

Free Energy Perturbation ◽

Rhodopseudomonas Viridis ◽

Relative Binding ◽

Energy Perturbation

Download Full-text

Development of a Quantum Mechanics-Based Free-Energy Perturbation Method: Use in the Calculation of Relative Solvation Free Energies

Journal of the American Chemical Society ◽

10.1021/ja049281r ◽

2004 ◽

Vol 126 (20) ◽

pp. 6224-6225 ◽

Cited By ~ 20

Author(s):

M. Rami Reddy ◽

U. C. Singh ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

Download Full-text

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-017-0075-9 ◽

2017 ◽

Vol 32 (1) ◽

pp. 21-44 ◽

Cited By ~ 14

Author(s):

Christina Athanasiou ◽

Sofia Vasilakaki ◽

Dimitris Dellis ◽

Zoe Cournia

Keyword(s):

Free Energy ◽

Free Energy Perturbation ◽

Grand Challenge ◽

Binding Affinities ◽

Relative Binding ◽

Energy Perturbation

Download Full-text

Correction to “Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States”

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.9b00841 ◽

2019 ◽

Vol 15 (10) ◽

pp. 5758-5758 ◽

Cited By ~ 3

Author(s):

César de Oliveira ◽

Haoyu S. Yu ◽

Wei Chen ◽

Robert Abel ◽

Lingle Wang

Keyword(s):

Free Energy ◽

Free Energy Perturbation ◽

Perturbation Approach ◽

Binding Affinities ◽

Relative Binding ◽

Energy Perturbation

Download Full-text

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose-1,6-bisphosphatase inhibitors

Journal of Computational Chemistry ◽

10.1002/jcc.21791 ◽

2011 ◽

Vol 32 (10) ◽

pp. 2097-2103 ◽

Cited By ~ 2

Author(s):

R.S. Rathore ◽

P. Aparoy ◽

P. Reddanna ◽

A. K. Kondapi ◽

M. Rami Reddy

Keyword(s):

Free Energy ◽

Md Simulation ◽

Free Energy Perturbation ◽

Free Energies ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation ◽

Binding Free Energies

Download Full-text

Free Energy Perturbation Calculations of the Relative Binding Affinities of an 8-Subunit Cavitand for Alkali Ions in Methanol

Journal of the American Chemical Society ◽

10.1021/ja00087a034 ◽

1994 ◽

Vol 116 (8) ◽

pp. 3449-3452 ◽

Cited By ~ 6

Author(s):

Bert E. IV Thomas ◽

Peter A. Kollman

Keyword(s):

Free Energy ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Alkali Ions ◽

Relative Binding ◽

Energy Perturbation

Download Full-text

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions

Journal of Computational Chemistry ◽

10.1002/jcc.21653 ◽

2010 ◽

Vol 32 (5) ◽

pp. 778-786 ◽

Cited By ~ 12

Author(s):

Kenji Hori ◽

Toru Yamaguchi ◽

Keita Uezu ◽

Michinori Sumimoto

Keyword(s):

Monte Carlo ◽

Free Energy ◽

Monte Carlo Simulations ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Quantum Mechanical ◽

Quantum Mechanical Calculations ◽

Energy Perturbation

Download Full-text