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List of works by Julian Tirado-Rives

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

scientific article

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

scientific article published in October 2003

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

scientific article published on 14 November 2017

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

scientific article

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

scientific article published on 9 May 2013

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

scientific article

Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields ⬇️

scientific article published on May 13, 2013

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

scientific article published in October 2006

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

scientific article

Determination of partial molar volumes from free energy perturbation theory

scientific article published on 15 January 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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 08 May 2018

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

scientific article published on 17 January 2014

Evaluation of CM5 Charges for Condensed-Phase Modeling.

scientific article

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

scientific article published on 13 October 2020

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

scientific article

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

scientific article published on 22 February 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

scientific article published on 19 June 2017

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field

scientific article published in June 2015

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

scientific article published on 16 February 2017

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

scientific article published on November 14, 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

scientific article published in June 2003

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

scientific article published on 21 April 2017

Methyl effects on protein-ligand binding

scientific article

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 ⬇️

scientific article published on May 8, 2003

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

scientific article

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

scientific article

Monte Carlo vs Molecular Dynamics for Conformational Sampling

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

scientific article published on 28 June 2008

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

scientific article published on 12 December 2012

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

scientific article published on 21 July 2016

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

scientific article

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

scientific article

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

scientific article published in July 2002

Prediction of the water content in protein binding sites

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in April 2004

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

scientific article published on October 14, 2010

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

scientific article published on 03 January 2019

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

scientific article

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

scientific article

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

scientific article published on 24 December 2008

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

scientific article published on October 26, 2012

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