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Journal of Chemical Information and Modeling
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March 18, 2025
Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations
Tomás F D Silva, Giovanni Bussi
Journal of Chemical Theory and Computation
|
October 18, 2022
Increasing the Realism of <i>in Silico</i> pHLIP Peptide Models with a Novel pH Gradient CpHMD Method
Tomás F D Silva, Diogo Vila-Viçosa, Miguel Machuqueiro
Journal of Chemical Theory and Computation
|
June 11, 2021
Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides
Tomás F D Silva, Diogo Vila-Viçosa, Miguel Machuqueiro
Cells
|
May 1, 2020
The Lysosomotropic Activity of Hydrophobic Weak Base Drugs is Mediated via Their Intercalation into the Lysosomal Membrane
Michal Stark, Tomás F D Silva, Guy Levin, et al.
Methods in Molecular Biology (Clifton, N.J.)
|
July 24, 2021
pK <sub>a</sub> Calculations in Membrane Proteins from Molecular Dynamics Simulations
Nuno F B Oliveira, Tomás F D Silva, Pedro B P S Reis, et al.
Journal of Chemical Information and Modeling
|
July 3, 2023
Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides
Tomás F D Silva, Hannah Visca, Craig Klumpp, et al.
Journal of Chemical Theory and Computation
|
May 8, 2018
Membrane-Induced p K<sub>a</sub> Shifts in wt-pHLIP and Its L16H Variant
Diogo Vila-Viçosa, Tomás F D Silva, Gregory Slaybaugh, et al.
Biorxiv : the Preprint Server for Biology
|
February 27, 2026
pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing
Danea Palmer, Adrien Chauvier, Tomás F D Silva, et al.
Journal of Chemical Theory and Computation
|
October 26, 2018
The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field
Tomás F D Silva, Diogo Vila-Viçosa, Pedro B P S Reis, et al.
Computational and Structural Biotechnology Journal
|
August 11, 2022
Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase
Patrícia T Borges, Diogo Silva, Tomás F D Silva, et al.
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Search research articles
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Showing results (1-10 of 13) with videos related to
Sort By:
Page
of 2
Journal of Chemical Information and Modeling
|
March 18, 2025
Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations
Tomás F D Silva, Giovanni Bussi
Journal of Chemical Theory and Computation
|
October 18, 2022
Increasing the Realism of <i>in Silico</i> pHLIP Peptide Models with a Novel pH Gradient CpHMD Method
Tomás F D Silva, Diogo Vila-Viçosa, Miguel Machuqueiro
Journal of Chemical Theory and Computation
|
June 11, 2021
Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides
Tomás F D Silva, Diogo Vila-Viçosa, Miguel Machuqueiro
Cells
|
May 1, 2020
The Lysosomotropic Activity of Hydrophobic Weak Base Drugs is Mediated via Their Intercalation into the Lysosomal Membrane
Michal Stark, Tomás F D Silva, Guy Levin, et al.
Methods in Molecular Biology (Clifton, N.J.)
|
July 24, 2021
pK <sub>a</sub> Calculations in Membrane Proteins from Molecular Dynamics Simulations
Nuno F B Oliveira, Tomás F D Silva, Pedro B P S Reis, et al.
Journal of Chemical Information and Modeling
|
July 3, 2023
Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides
Tomás F D Silva, Hannah Visca, Craig Klumpp, et al.
Journal of Chemical Theory and Computation
|
May 8, 2018
Membrane-Induced p K<sub>a</sub> Shifts in wt-pHLIP and Its L16H Variant
Diogo Vila-Viçosa, Tomás F D Silva, Gregory Slaybaugh, et al.
Biorxiv : the Preprint Server for Biology
|
February 27, 2026
pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing
Danea Palmer, Adrien Chauvier, Tomás F D Silva, et al.
Journal of Chemical Theory and Computation
|
October 26, 2018
The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field
Tomás F D Silva, Diogo Vila-Viçosa, Pedro B P S Reis, et al.
Computational and Structural Biotechnology Journal
|
August 11, 2022
Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase
Patrícia T Borges, Diogo Silva, Tomás F D Silva, et al.
Page
of 2