Karim Malekzadeh

Enhanced-sampling simulations reveal distinct intermediates in SARS-CoV-2 FSE pseudoknot interconversion

Karim Malekzadeh, Mangesh Bhendale, Gül H. Zerze

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Stabilizing Effect of Neighboring Disordered RGG Domain on the Folded State of FUS-RRM

Kosar Rahimi, Ayush Gupta, Karim Malekzadeh, Gül H. Zerze

, and the KK loop through a network of targeted multivalent contacts between the RGG and RRM residues. This work reveals how a disordered region stabilizes a folded RNA-binding domain, underscoring the importance of disordered-ordered interdomain coupling in shaping the folding landscape …

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BPS2026 – Synergistic role of RGG2 in modulating FUS RRM structure and RNA binding revealed by enhanced sampling simulations

Kosar Rahimi, Ayush Gupta, Karim Malekzadeh, Gül H. Zerze

BPS2026 – Modulation of FUS RRM folding by neighboring disordered regions

Kosar Rahimi, Ayush Gupta, Karim Malekzadeh, Gül H. Zerze

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Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki et autres

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and …

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Blind prediction of complex water and ion ensembles around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki et autres

Abstract Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water …

us, it, pl, se, in, jp, cn, cl, be (code pays fourni par la source)

Author response for "Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 "

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki et autres

Optimizing On-the-Fly Probability Enhanced Sampling for Complex RNA Systems: Sampling Free Energy Surfaces of an H-Type Pseudoknot

Karim Malekzadeh, Gül H. Zerze

All-atom molecular dynamics (MD) simulations offer crucial insights into biomolecular dynamics, but inherent time scale constraints often limit their effectiveness. Advanced sampling techniques help overcome these limitations, enabling predictions of deeply rugged folding free energy surfaces (FES) of RNA at atomistic resolution. …

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BPS2025 - The dynamic interplay of stability and flexibility: Unraveling the role of pseudoknot 1 in tmRNA trans-translation

Karim Malekzadeh, Gül H. Zerze

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Optimizing On-the-Fly Probability Enhanced Sampling for Complex RNA Systems: Sampling Free Energy Surfaces of an H-Type Pseudoknot

Karim Malekzadeh, Gül H. Zerze

Abstract All-atom molecular dynamics (MD) simulations offer crucial insights into biomolecular dynamics, but inherent time scale constraints often limit their effectiveness. Advanced sampling techniques help overcome these limitations, enabling predictions of deeply rugged folding free energy surfaces (FES) of RNAs at atomistic …

us (code pays fourni par la source)