Modesto Orozco
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View article: Success and Limitations of Current Force Fields for the Description of RNA–Ligand Complexes
Success and Limitations of Current Force Fields for the Description of RNA–Ligand Complexes Open
We present a systematic assessment of the last generation of RNA force fields to reproduce the structures and dynamics of ligand-RNA complexes. Our comprehensive analysis helped not only to define the more reliable force field to represent…
View article: Molecular simulations meet personalized medicine: The mechanism of action of CLC-5 antiporter and the origin of Dent's disease
Molecular simulations meet personalized medicine: The mechanism of action of CLC-5 antiporter and the origin of Dent's disease Open
ClC-5 is a Cl−/H+ antiporter crucial for the homeostasis of the entire organism, and whose functional deficiencies cause pathologies such as Dent's disease, a rare genetic disorder that can have lethal consequences. While the clinical aspe…
View article: Dually-decorated palmitate-containing lipid nanoparticles for the targeted delivery of siRNAs against HER2 and Hsp27 in HER2+ breast cancer
Dually-decorated palmitate-containing lipid nanoparticles for the targeted delivery of siRNAs against HER2 and Hsp27 in HER2+ breast cancer Open
Ionizable lipid nanoparticles (LNPs) have enabled significant advances in oligonucleotide therapeutics, culminating in the clinical approval of an siRNA-based formulation. Unfortunately, practical use of siRNA containing LNPs is still hamp…
View article: Investigating mu and alpha oscillations as indicators of intra-individual success and inter-individual ability in motor imagery performance
Investigating mu and alpha oscillations as indicators of intra-individual success and inter-individual ability in motor imagery performance Open
Mu and alpha rhythms (8–14 Hz) are recognized for their suppression during motor execution and imagery tasks. Recent research suggests that these oscillations might also serve as a marker of successful motor imagery (MI) performance. This …
View article: CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers Open
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein–DN…
View article: Reply to “Comment on ‘Main role of fractal-like nature of conformational space in subdiffusion in proteins' ”
Reply to “Comment on ‘Main role of fractal-like nature of conformational space in subdiffusion in proteins' ” Open
We present here the response to the criticisms raised by Neusius This paper contains new results and analyses which, we believe, clarify and strengthen the findings of Maggi [] and make them even more general.
View article: Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes
Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes Open
G-quadruplex (G4) nucleic acid ligands have attracted significant attention as putative anticancer agents for selectively stabilizing telomeric structures. In our pursuit of targeting the most biologically relevant telomeric structures, we…
View article: Gromologist: A GROMACS-oriented utility library for structure and topology manipulation
Gromologist: A GROMACS-oriented utility library for structure and topology manipulation Open
Despite the increasing automation of workflows for the preparation of systems for molecular dynamics simulations, the custom editing of molecular topologies to accommodate non-standard modifications remains a daunting task even for experie…
View article: Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism
Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism Open
By combining in silico, biophysical, and in vitro experiments, we decipher the topology, physical, and potential biological properties of hybrid-parallel nucleic acids triplexes, an elusive structure at the basis of life. We found that hyb…
View article: Flexibility in PAM recognition expands DNA targeting in xCas9
Flexibility in PAM recognition expands DNA targeting in xCas9 Open
xCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognising a series of alternative …
View article: Author response: Flexibility in PAM recognition expands DNA targeting in xCas9
Author response: Flexibility in PAM recognition expands DNA targeting in xCas9 Open
View article: Author response: Flexibility in PAM Recognition Expands DNA Targeting in xCas9
Author response: Flexibility in PAM Recognition Expands DNA Targeting in xCas9 Open
View article: Flexibility in PAM Recognition Expands DNA Targeting in xCas9
Flexibility in PAM Recognition Expands DNA Targeting in xCas9 Open
xCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognizing a series of alternative …
View article: The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the <scp>L-</scp>amino acid transporters
The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the <span>L-</span>amino acid transporters Open
L-Amino acid transporters (LATs) play a key role in a wide range of physiological processes. Defects in LATs can lead to neurological disorders and aminoacidurias, while the overexpression of these transporters is related to cancer. BasC i…
View article: Flexibility in PAM recognition expands DNA targeting in xCas9
Flexibility in PAM recognition expands DNA targeting in xCas9 Open
xCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognising a series of alternative …
View article: Mechanism of expanded DNA recognition in xCas9
Mechanism of expanded DNA recognition in xCas9 Open
xCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognizing a series of alternative …
View article: Stevens-Johnson Syndrome secondary to nivolumab in a patient with mixed cell variety classical Hodgkin Lymphoma
Stevens-Johnson Syndrome secondary to nivolumab in a patient with mixed cell variety classical Hodgkin Lymphoma Open
The immune checkpoint inhibitors (ICIs) nivolumab and pembrolizumab are some of the principal treatment options for relapsed or refractory classic Hodgkin lymphoma. However, immunotherapy has been related to dermatological adverse events (…
View article: SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis Open
View article: RNA dynamics from experimental and computational approaches
RNA dynamics from experimental and computational approaches Open
View article: Flexibility in PAM Recognition Expands DNA Targeting in xCas9
Flexibility in PAM Recognition Expands DNA Targeting in xCas9 Open
xCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognizing a series of alternative …
View article: An integrated machine-learning model to predict nucleosome architecture
An integrated machine-learning model to predict nucleosome architecture Open
We demonstrate that nucleosomes placed in the gene body can be accurately located from signal decay theory assuming two emitters located at the beginning and at the end of genes. These generated wave signals can be in phase (leading to wel…
View article: Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange
Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange Open
The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials a…
View article: Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows Open
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompani…
View article: Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions
Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions Open
Recent findings in cell biology have rekindled interest in Z-DNA, the left-handed helical form of DNA. We report here that two minimally modified nucleosides, 2′F-araC and 2′F-riboG, induce the formation of the Z-form under low ionic stren…
View article: SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis Open
SUMMARY SETD8 is a methyltransferase that is overexpressed in several cancers, which monomethylates H4K20 as well as other non-histone targets such as PCNA or p53. We here report novel SETD8 inhibitors, which were discovered while trying t…
View article: Special issue: Multiscale simulations of DNA from electrons to nucleosomes
Special issue: Multiscale simulations of DNA from electrons to nucleosomes Open
View article: CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes Open
We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are …
View article: Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism
Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism Open
By combining in-silico , biophysical and in-cellulo experiments, we decipher the topology, physical and potential biological properties of hybrid-parallel nucleic acids triplexes; an elusive structure at the basis of life. We found that hy…
View article: MD-DATA: the legacy of the ABC Consortium
MD-DATA: the legacy of the ABC Consortium Open
The ABC Consortium has been generating nucleic-acids MD trajectories for more than 20 years. This brief comment highlights the importance of this data for the field, which triggered a number of critical studies, including force-field param…
View article: RNA Dynamics from Experimental and Computational Approaches
RNA Dynamics from Experimental and Computational Approaches Open
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…