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View article: The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH
The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH Open
We present the nuclear magnetic resonance spectroscopy (NMR) solution structure of the 5'-terminal stem loop 5_SL1 (SL1) of the SARS-CoV-2 genome. SL1 contains two A-form helical elements and two regions with non-canonical structure, namel…
View article: Improving Inverse Folding models at Protein Stability Prediction without additional Training or Data
Improving Inverse Folding models at Protein Stability Prediction without additional Training or Data Open
Deep learning protein sequence models have shown outstanding performance at de novo protein design and variant effect prediction. We substantially improve performance without further training or use of additional experimental data by intro…
View article: The 5′-terminal stem–loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH
The 5′-terminal stem–loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH Open
We present the nuclear magnetic resonance spectroscopy (NMR) solution structure of the 5′-terminal stem loop 5_SL1 (SL1) of the SARS-CoV-2 genome. SL1 contains two A-form helical elements and two regions with non-canonical structure, namel…
View article: Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop
Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop Open
Both experimental and theoretical structure determinations of RNAs have remained challenging due to the intrinsic dynamics of RNAs. We report here an integrated nuclear magnetic resonance/molecular dynamics (NMR/MD) structure determination…
View article: Discovering functionally important sites in proteins
Discovering functionally important sites in proteins Open
Proteins play important roles in biology, biotechnology and pharmacology, and missense variants are a common cause of disease. Discovering functionally important sites in proteins is a central but difficult problem because of the lack of l…
View article: LLM-PBC: Logic Learning Machine-Based Explainable Rules Accurately Stratify the Genetic Risk of Primary Biliary Cholangitis
LLM-PBC: Logic Learning Machine-Based Explainable Rules Accurately Stratify the Genetic Risk of Primary Biliary Cholangitis Open
Background: The application of Machine Learning (ML) to genetic individual-level data represents a foreseeable advancement for the field, which is still in its infancy. Here, we aimed to evaluate the feasibility and accuracy of an ML-based…
View article: Discovering functionally important sites in proteins
Discovering functionally important sites in proteins Open
Proteins play important roles in biology, biotechnology and pharmacology, and missense variants are a common cause of disease. Discovering functionally important sites in proteins is a central but difficult problem because of the lack of l…
View article: Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments Open
We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like …
View article: MEDTEC Students against Coronavirus: Investigating the Role of Hemostatic Genes in the Predisposition to COVID-19 Severity
MEDTEC Students against Coronavirus: Investigating the Role of Hemostatic Genes in the Predisposition to COVID-19 Severity Open
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Besides virus intrinsic characteristics, the host genetic makeup is predicted to account for the extre…
View article: Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations
Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations Open
The 5′ untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structur…
View article: Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations Open
Nanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two smal…
View article: Author response: Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
Author response: Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations Open
Article Figures and data Abstract Introduction Results and discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Nanodiscs are membrane mimetics that c…
View article: Integrating NMR and simulations reveals motions in the UUCG tetraloop
Integrating NMR and simulations reveals motions in the UUCG tetraloop Open
We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem–loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements da…
View article: Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution Open
Many proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domai…
View article: Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop
Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop Open
Trajectory and other datafile associated to the paper Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop Manuscript available HERE Code and instructions on github available HERE
View article: Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution Open
Many proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domai…
View article: Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations Open
Nanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two smal…
View article: Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop
Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop Open
We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem-loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements da…
View article: Barnaba: software for analysis of nucleic acid structures and trajectories
Barnaba: software for analysis of nucleic acid structures and trajectories Open
RNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The …
View article: Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy reweighting approach
Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy reweighting approach Open
We describe a Bayesian/Maximum entropy (BME) procedure and software to construct a conformational ensemble of a biomolecular system by integrating molecular simulations and experimental data. First, an initial conformational ensemble is co…
View article: Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories
Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories Open
RNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The …
View article: Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations Open
Combining molecular simulations with NMR spectroscopy enables reconstruction of RNA tetranucleotide conformational ensembles.
View article: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview Open
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in pa…
View article: Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations
Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations Open
We determine the conformational ensemble of four RNA tetranucleotides by using available nuclear magnetic spectroscopy data in conjunction with extensive atomistic molecular dynamics simulations. This combination is achieved by applying a …