Lista de obras - Julian Tirado-Rives - Dominio Público Uruguay

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations

artículo científico publicado en 2017

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor

scientific article published on 07 October 2019

Activity predictions for efavirenz analogues with the K103N mutant of HIV reverse transcriptase

artículo científico publicado en 2003

Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor

artículo científico publicado en 2017

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

artículo científico publicado en 2015

Bifunctional inhibition of human immunodeficiency virus type 1 reverse transcriptase: mechanism and proof-of-concept as a novel therapeutic design strategy

artículo científico publicado en 2013

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

artículo científico publicado en 2016

Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields

artículo científico publicado en 2013

Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding

artículo científico publicado en 2006

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.

artículo científico publicado en 2003

Determination of partial molar volumes from free energy perturbation theory

artículo científico publicado en 2015

Development and Testing of the OPLS-AA/M Force Field for RNA

scientific article published on 12 March 2019

Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures

artículo científico publicado en 2009

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

artículo científico publicado en 2010

Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz

artículo científico publicado en 2007

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

scientific article published on October 2009

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding

artículo científico publicado en 2018

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

artículo científico publicado en 2014

Evaluation of CM5 Charges for Condensed-Phase Modeling.

artículo científico publicado en 2014

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

artículo científico publicado en 2020

Exploiting Structural Analysis, in Silico Screening, and Serendipity To Identify Novel Inhibitors of Drug-Resistant Falciparum Malaria

artículo científico publicado en 2009

Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water

artículo científico publicado en 2016

Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2

scientific article published on 28 August 2020

Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization

artículo científico publicado en 2017

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field

artículo científico publicado en 2015

Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field

artículo científico publicado en 2017

Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model ⬇️

artículo científico publicado el 14 de noviembre de 2011

In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX

scientific article published on May 2009

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations

artículo científico publicado en 2003

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

artículo científico publicado en 2017

Methyl effects on protein-ligand binding

artículo científico publicado en 2012

Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination

article

Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Aryl-Substituted Benzimidazole Analogues ⬇️

artículo científico publicado el 8 de mayo de 2003

Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design

artículo científico publicado en 2014

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

artículo científico publicado en 2005

Monte Carlo vs Molecular Dynamics for Conformational Sampling

Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations

artículo científico publicado en 2008

Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase to enhance Y181C potency

artículo científico publicado en 2012

Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System

artículo científico publicado en 2016

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

artículo científico publicado en 2005

Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method

artículo científico publicado en 1998

Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations

artículo científico publicado en 2002

Prediction of the water content in protein binding sites

artículo científico publicado en 2009

QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory

scientific article published on 27 June 2019

Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water

artículo científico publicado en 2010

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

artículo científico publicado en 2005

Robust Free Energy Perturbation Protocols for Creating Molecules in Solution

scientific article published on 24 June 2019

Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring

artículo científico publicado en 2007

Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analogues

artículo científico publicado en 2004

Synthesis and Evaluation of Selected Key Methyl Ether Derivatives of Vancomycin Aglycon ⬇️

artículo científico publicado el 14 de octubre de 2010

Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase

artículo científico publicado en 2019

Validation of a model for the complex of HIV-1 reverse transcriptase with nonnucleoside inhibitor TMC125.

artículo científico publicado en 2003

Vancomycin analogs: Seeking improved binding of d-Ala-d-Ala and d-Ala-d-Lac peptides by side-chain and backbone modifications

artículo científico publicado en 2009

Vancomycin resistance: modeling backbone variants with D-Ala-D-Ala and D-Ala-D-Lac peptides

artículo científico publicado en 2008

Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum Macrophage Migration Inhibitory Factor ⬇️

artículo científico publicado el 26 de octubre de 2012

Lista de obras de Julian Tirado-Rives

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor

Activity predictions for efavirenz analogues with the K103N mutant of HIV reverse transcriptase

Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

Bifunctional inhibition of human immunodeficiency virus type 1 reverse transcriptase: mechanism and proof-of-concept as a novel therapeutic design strategy

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields

Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.

Determination of partial molar volumes from free energy perturbation theory

Development and Testing of the OPLS-AA/M Force Field for RNA

Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

Evaluation of CM5 Charges for Condensed-Phase Modeling.

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

Exploiting Structural Analysis, in Silico Screening, and Serendipity To Identify Novel Inhibitors of Drug-Resistant Falciparum Malaria

Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water

Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2

Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field

Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field

Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model ⬇️

In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

Methyl effects on protein-ligand binding

Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination

Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Aryl-Substituted Benzimidazole Analogues ⬇️

Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Monte Carlo vs Molecular Dynamics for Conformational Sampling

Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations

Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase to enhance Y181C potency

Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method

Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations

Prediction of the water content in protein binding sites

QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory

Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

Robust Free Energy Perturbation Protocols for Creating Molecules in Solution

Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring

Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analogues

Synthesis and Evaluation of Selected Key Methyl Ether Derivatives of Vancomycin Aglycon ⬇️

Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase

Validation of a model for the complex of HIV-1 reverse transcriptase with nonnucleoside inhibitor TMC125.

Vancomycin analogs: Seeking improved binding of d-Ala-d-Ala and d-Ala-d-Lac peptides by side-chain and backbone modifications

Vancomycin resistance: modeling backbone variants with D-Ala-D-Ala and D-Ala-D-Lac peptides

Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum Macrophage Migration Inhibitory Factor ⬇️