Lista de obras - Thom Vreven - Dominio Público Uruguay

A machine learning approach for the prediction of protein surface loop flexibility ⬇️

artículo científico publicado el 1 de junio de 2011

Ab InitioPhotoisomerization Dynamics of a Simple Retinal Chromophore Model

artículo científico publicado en 1997

An ab initio study of the photochemical decomposition of 3, 3-dimethyldiazirine

Beyond the Continuum Approach

Binding interface prediction by combining protein-protein docking results ⬇️

artículo científico publicado el 31 de agosto de 2013

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

artículo científico publicado en 2013

Combining Microsolvation and Polarizable Continuum Studies: New Insights in the Rotation Mechanism of Amides in Water

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

artículo científico publicado en 2006

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

artículo científico publicado en 2011

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

artículo científico publicado en 2013

Computational investigation into the fluorescence of luciferin analogues

artículo científico publicado en 2019

Density functional study of the optical rotation of glucose in aqueous solution

artículo científico publicado en 2004

Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study

artículo científico publicado en 2005

Evaluating template-based and template-free protein-protein complex structure prediction ⬇️

artículo científico publicado el 1 de julio de 2013

Exploring Angular Distance in Protein-Protein Docking Algorithms ⬇️

artículo científico publicado el 21 de febrero de 2013

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints

artículo científico publicado en 2003

Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach

artículo científico publicado en 2004

Implementation and benchmark tests of the DFTB method and its application in the ONIOM method

article published in 2009

Integrating atom‐based and residue‐based scoring functions for protein–protein docking ⬇️

artículo científico publicado el 8 de agosto de 2011

Integrating cross-linking experiments with ab initio protein-protein docking

artículo científico publicado en 2018

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study

artículo científico publicado en 2006

Link atom bond length effect in ONIOM excited state calculations

artículo científico publicado en 2010

Lysine carboxylation in proteins: OXA-10 beta-lactamase

artículo científico publicado en 2005

Modeling Photochemical [4 + 4] Cycloadditions: Conical Intersections Located with CASSCF for Butadiene + Butadiene

artículo científico publicado en 1997

Modeling Proton Transfer in Zeolites: Convergence Behavior of Embedded and Constrained Cluster Calculations

artículo científico publicado en 2005

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes

artículo científico publicado en 2014

Oscillator Strengths in ONIOM Excited State Calculations

artículo científico publicado en 2010

Performance Evaluation of the Three-Layer ONIOM Method: Case Study for a Zwitterionic Peptide

artículo científico publicado en 2006

Performance of ZDOCK and IRAD in CAPRI rounds 28-34.

artículo científico publicado en 2016

Performance of ZDOCK and IRAD in CAPRI rounds 39-45

artículo científico publicado en 2020

Performance of ZDOCK in CAPRI rounds 20-26.

artículo científico publicado en 2013

Photoisomerization Path for a Realistic Retinal Chromophore Model: The Nonatetraeniminium Cation

artículo científico publicado en 1998

Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects

artículo científico publicado en 1998

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

artículo científico publicado en 2016

Prediction of protein–protein binding free energies ⬇️

artículo científico publicado el 2 de febrero de 2012

Protein–protein docking benchmark version 4.0 ⬇️

artículo científico publicado el 15 de noviembre de 2010

QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework

artículo científico publicado en 2008

Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D.

artículo científico publicado en 2008

The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution

article

Theoretical Study of the 1,2 Rearrangement of Housane Radical Cations: Key Role of a Transient Cyclopentane-1,3-diyl Intermediate

artículo científico publicado en 1999

Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181.

artículo científico publicado en 2008

UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery

artículo científico publicado en 2012

Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines

scientific article published in 2000

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

artículo científico publicado en 2015

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree-Fock

artículo científico publicado en 2009

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

artículo científico publicado en 2014

Lista de obras de Thom Vreven

A machine learning approach for the prediction of protein surface loop flexibility ⬇️

Ab InitioPhotoisomerization Dynamics of a Simple Retinal Chromophore Model

An ab initio study of the photochemical decomposition of 3, 3-dimethyldiazirine

Beyond the Continuum Approach

Binding interface prediction by combining protein-protein docking results ⬇️

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Blind prediction of interfacial water positions in CAPRI

Combining Microsolvation and Polarizable Continuum Studies: New Insights in the Rotation Mechanism of Amides in Water

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Computational investigation into the fluorescence of luciferin analogues

Density functional study of the optical rotation of glucose in aqueous solution

Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study

Evaluating template-based and template-free protein-protein complex structure prediction ⬇️

Exploring Angular Distance in Protein-Protein Docking Algorithms ⬇️

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints

Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach

Implementation and benchmark tests of the DFTB method and its application in the ONIOM method

Integrating atom‐based and residue‐based scoring functions for protein–protein docking ⬇️

Integrating cross-linking experiments with ab initio protein-protein docking

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study

Link atom bond length effect in ONIOM excited state calculations

Lysine carboxylation in proteins: OXA-10 beta-lactamase

Modeling Photochemical [4 + 4] Cycloadditions: Conical Intersections Located with CASSCF for Butadiene + Butadiene

Modeling Proton Transfer in Zeolites: Convergence Behavior of Embedded and Constrained Cluster Calculations

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes

Oscillator Strengths in ONIOM Excited State Calculations

Performance Evaluation of the Three-Layer ONIOM Method: Case Study for a Zwitterionic Peptide

Performance of ZDOCK and IRAD in CAPRI rounds 28-34.

Performance of ZDOCK and IRAD in CAPRI rounds 39-45

Performance of ZDOCK in CAPRI rounds 20-26.

Photoisomerization Path for a Realistic Retinal Chromophore Model: The Nonatetraeniminium Cation

Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Prediction of protein–protein binding free energies ⬇️

Protein–protein docking benchmark version 4.0 ⬇️

QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework

Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D.

The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution

Theoretical Study of the 1,2 Rearrangement of Housane Radical Cations: Key Role of a Transient Cyclopentane-1,3-diyl Intermediate

Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181.

UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery

Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree-Fock

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers