Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase

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Computational Molecular Bioscience

ISSN Print: 2165-3445
ISSN Online: 2165-3453
www.scirp.org/journal/cmb
E-mail: cmb@scirp.org

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"Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase"
written by Emilio Gallicchio,
published by Computational Molecular Bioscience, Vol.2 No.1, 2012

has been cited by the following article(s):

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CrossRef

[1]	Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints
	2021

[2]	On Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with …
	Journal of Chemical Information and Modeling, 2018

[3]	Analytical Model of the Free Energy of Alchemical Molecular Binding
	2018

[4]	Dihydropyrimidinone-isatin hybrids as novel non-nucleoside HIV-1 reverse transcriptase inhibitors
	Bioorganic Chemistry, 2017

[5]	Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories
	Journal of Chemical Theory and Computation, 2017

[6]	Alchemical Response Parameters from an Analytical Model of Molecular Binding
	2017

[7]	Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase
	ACS Omega, 2016

[8]	Recent advances in computational models for the study of protein–peptide interactions
	Advances in Protein Chemistry and Structural Biology, 2016

[9]	Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy …
	Journal of Chemical Theory and Computation, 2016

[10]	Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation
	Journal of chemical theory and computation, 2016

[11]	Chapter Two-Recent Advances in Computational Models for the Study of Protein–Peptide Interactions
	Advances in Protein Chemistry and Structural Biology, 2016

[12]	A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge
	Journal of Computer-Aided Molecular Design, 2016

[13]	A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors
	Protein Science, 2015

[14]	BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge
	Journal of computer-aided molecular design, 2015

[15]	Parameterization of an effective potential for protein–ligand binding from host–guest affinity data
	Journal of Molecular Recognition, 2015

[16]	Recent Advances in the Discovery and Development of Novel HIV-1 NNRTI Platforms (Part II): 2009-2013 Update#
	Current medicinal chemistry, 2014

[17]	Investigating the mutation resistance of nonnucleoside inhibitors of HIV‐RT using multiple microsecond atomistic simulations
	Proteins: Structure, Function, and Bioinformatics, 2014

[18]	Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge
	Journal of computer-aided molecular design, 2014

[19]	Recent advances in the discovery and development of novel HIV-1 NNRTI platforms (Part II): 2009-2013 update
	Current Medicinal Chemistry, 2014

[20]	Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process
	Journal of Chemical Theory and Computation, 2013

[1]	Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints Journal of Chemical Theory and Computation, 2021 DOI:10.1021/acs.jctc.0c01219

[2]	Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints Journal of Chemical Theory and Computation, 2021 DOI:10.1021/acs.jctc.0c01219

[3]	Analytical Model of the Free Energy of Alchemical Molecular Binding Journal of Chemical Theory and Computation, 2018 DOI:10.1021/acs.jctc.8b00967

[4]	Analytical Model of the Free Energy of Alchemical Molecular Binding Journal of Chemical Theory and Computation, 2018 DOI:10.1021/acs.jctc.8b00967

[5]	Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials Journal of Chemical Information and Modeling, 2018 DOI:10.1021/acs.jcim.8b00194

[6]	Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials Journal of Chemical Information and Modeling, 2018 DOI:10.1021/acs.jcim.8b00194

[7]	Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories Journal of Chemical Theory and Computation, 2017 DOI:10.1021/acs.jctc.6b01192

[8]	Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories Journal of Chemical Theory and Computation, 2017 DOI:10.1021/acs.jctc.6b01192

[9]	Dihydropyrimidinone-isatin hybrids as novel non-nucleoside HIV-1 reverse transcriptase inhibitors Bioorganic Chemistry, 2017 DOI:10.1016/j.bioorg.2017.01.006

[10]	Parameterization of an effective potential for protein-ligand binding from host-guest affinity data Journal of Molecular Recognition, 2016 DOI:10.1002/jmr.2489

[11]	Insights into Enzyme Mechanisms and Functions from Experimental and Computational Methods Advances in Protein Chemistry and Structural Biology, 2016 DOI:10.1016/bs.apcsb.2016.06.002

[12]	Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation Journal of Chemical Theory and Computation, 2016 DOI:10.1021/acs.jctc.6b00134

[13]	Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase ACS Omega, 2016 DOI:10.1021/acsomega.6b00123

[14]	Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase ACS Omega, 2016 DOI:10.1021/acsomega.6b00123

[15]	Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation Journal of Chemical Theory and Computation, 2016 DOI:10.1021/acs.jctc.6b00134

[16]	Parameterization of an effective potential for protein–ligand binding from host–guest affinity data Journal of Molecular Recognition, 2016 DOI:10.1002/jmr.2489

[17]	A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors Protein Science, 2015 DOI:10.1002/pro.2708

[18]	Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations Proteins: Structure, Function, and Bioinformatics, 2014 DOI:10.1002/prot.24346

[19]	Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process Journal of Chemical Theory and Computation, 2013 DOI:10.1021/ct400003r

[20]	Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process Journal of Chemical Theory and Computation, 2013 DOI:10.1021/ct400003r

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	+86 18163351462(WhatsApp)
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