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Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
TLDR
We use metadynamics simulations to investigate the isomerization of CA's model substrate HAGPIA in water and in its target protein CypA. Expand
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GABA binding to an insect GABA receptor: a molecular dynamics and mutagenesis study.
RDL receptors are GABA-activated inhibitory Cys-loop receptors found throughout the insect CNS. They are a key target for insecticides. Here, we characterize the GABA binding site in RDL receptorsExpand
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Molecular Dynamics Simulations of GABA Binding to the GABAC Receptor: The Role of Arg104
GABA is the major inhibitory neurotransmitter in the nervous system and acts at a variety of receptors including GABAC receptors, which are a subclass of GABAA receptors. Here we have used molecularExpand
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Promoting transparency and reproducibility in enhanced molecular simulations
TLDR
We disseminate protocols for enhanced-sampling molecular simulations by disseminating protocols for molecular simulations. Expand
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Glucose in Aqueous Solution by First Principles Molecular Dynamics
We present the results of the first ab initio molecular dynamics simulations, based on the Car−Parrinello method, of glucose in water, performed to investigate structural aspects of the anomericExpand
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Excited states of biological chromophores studied using many-body perturbation theory: Effects of resonant-antiresonant coupling and dynamical screening
The excited states of model chromophores of the photoactive yellow protein and of rhodopsin are studied using ab initio many-body perturbation theory (within the GW approximation and Bethe-SalpeterExpand
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Trans−cis Switching Mechanisms in Proline Analogues and Their Relevance for the Gating of the 5-HT3 Receptor
Trans−cis isomerization of a proline peptide bond is a potential mechanism to open the channel of the 5-HT3 receptor. Here, we have used the metadynamics method to theoretically explore such aExpand
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Structural Properties of Green Tea Catechins.
Green tea catechins are polyphenols which are believed to provide health benefits; they are marketed as health supplements and are studied for their potential effects on a variety of medicalExpand
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An Excited State Density Functional Theory Study of the Rhodopsin Chromophore
Using a recently developed scheme for performing, within density functional theory, molecular dynamics and geometry optimization for fairly large systems in the first excited singlet state, we haveExpand
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Rapid desensitization of the rat α7 nAChR is facilitated by the presence of a proline residue in the outer β‐sheet
The rat α7 nicotinic acetylcholine receptor (nAChR) has a proline residue near the middle of the β9 strand. The replacement of this proline residue at position 180 (P180) by either threonineExpand
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