List of works - Jeffry D. Madura

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter

scientific article

An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research

scientific article published on January 2006

Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors

scientific article published on 4 April 2010

CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment

article

Computational and Experimental Determination of the α-Helix Unfolding Reaction Coordinate†

scientific article published on 12 January 2008

Conformational Free-Energy Landscapes for a Peptide in Saline Environments ⬇️

scientific article published on December 18, 2012

Contributors

Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25.

scientific article

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

scientific article (publication date: 22 May 2004)

Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore.

scientific article

Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter

scientific article

Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase

scientific article published in December 2002

Docking of sulfonamides to carbonic anhydrase II and IV.

scientific article published on June 2000

Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template

scientific article published in February 2008

Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase

scientific article

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

article

Exploring the Physicochemical Properties of Oxime-Reactivation Therapeutics for Cyclosarin, Sarin, Tabun, and VX Inactivated Acetylcholinesterase

scientific article published on 09 January 2014

Family 18 chitolectins: comparison of MGP40 and HUMGP39

scientific article

Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase

scientific article published on October 2013

HIV-1 RT nonnucleoside inhibitors and their interaction with RT for antiviral drug development.

scientific article published on December 2006

Identification of a novel selective serotonin reuptake inhibitor by coupling monoamine transporter-based virtual screening and rational molecular hybridization

scientific article

Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters.

scientific article

Interaction of the phospholipid head group with representative quartz and aluminosilicate structures: an ab initio study

journal article published in 2008

Kinetic and docking studies of the interaction of quinones with the quinone reductase active site

scientific article published in February 2003

Kinetic and mechanistic studies of prolyl oligopeptidase from the hyperthermophile Pyrococcus furiosus

scientific article

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis

scientific article

Mechanisms underlying taurine-mediated alterations in membrane function

scientific article published in September 1995

Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding

scientific article

Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer

scientific article published in March 2010

Monoamine transporter structure, function, dynamics, and drug discovery: a computational perspective.

scientific article

New design strategies for antidepressant drugs.

scientific article published on 31 August 2013

Receptor-Based Discovery of a Plasmalemmal Monoamine Transporter Inhibitor via High Throughput Docking and Pharmacophore Modeling

scientific article

Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.

scientific article

Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS

article

Salt dependence of an alpha-helical peptide folding energy landscapes

scientific article published on November 2009

Scanning electron microscopy and molecular modeling of inhibition of calcium oxalate monohydrate crystal growth by citrate and phosphocitrate

scientific article published on 01 April 1995

Sodium perchlorate effects on the helical stability of a mainly alanine peptide

scientific article

Solubility of simple, nonpolar compounds in TIP4P-Ew

scientific article published on 01 January 2006

Solution Structural Ensembles of Substrate-Free Cytochrome P450 cam

scientific article

Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam

scientific article

Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design

article

Structure of aqueous sodium perchlorate solutions

scientific article published in December 2008

The JMGM/MGMS graphics prize

scientific article

Topical perspectives

scientific article published on 22 July 2010

β-Amyloid and Neprilysin Computational Studies Identify Critical Residues Implicated in Binding Specificity

scientific article published on 31 March 2014

List of works by Jeffry D. Madura

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter

An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research

Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors

CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment

Computational and Experimental Determination of the α-Helix Unfolding Reaction Coordinate†

Conformational Free-Energy Landscapes for a Peptide in Saline Environments ⬇️

Contributors

Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25.

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore.

Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter

Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase

Docking of sulfonamides to carbonic anhydrase II and IV.

Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template

Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

Exploring the Physicochemical Properties of Oxime-Reactivation Therapeutics for Cyclosarin, Sarin, Tabun, and VX Inactivated Acetylcholinesterase

Family 18 chitolectins: comparison of MGP40 and HUMGP39

Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase

HIV-1 RT nonnucleoside inhibitors and their interaction with RT for antiviral drug development.

Identification of a novel selective serotonin reuptake inhibitor by coupling monoamine transporter-based virtual screening and rational molecular hybridization

Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters.

Interaction of the phospholipid head group with representative quartz and aluminosilicate structures: an ab initio study

Kinetic and docking studies of the interaction of quinones with the quinone reductase active site

Kinetic and mechanistic studies of prolyl oligopeptidase from the hyperthermophile Pyrococcus furiosus

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis

Mechanisms underlying taurine-mediated alterations in membrane function

Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding

Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer

Monoamine transporter structure, function, dynamics, and drug discovery: a computational perspective.

New design strategies for antidepressant drugs.

Receptor-Based Discovery of a Plasmalemmal Monoamine Transporter Inhibitor via High Throughput Docking and Pharmacophore Modeling

Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.

Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS

Salt dependence of an alpha-helical peptide folding energy landscapes

Scanning electron microscopy and molecular modeling of inhibition of calcium oxalate monohydrate crystal growth by citrate and phosphocitrate

Sodium perchlorate effects on the helical stability of a mainly alanine peptide

Solubility of simple, nonpolar compounds in TIP4P-Ew

Solution Structural Ensembles of Substrate-Free Cytochrome P450 cam

Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam

Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design

Structure of aqueous sodium perchlorate solutions

The JMGM/MGMS graphics prize

Topical perspectives

β-Amyloid and Neprilysin Computational Studies Identify Critical Residues Implicated in Binding Specificity