Fabian Rudolf | Searcharxiv

arXiv2025

The Reproducible Research Platform establishes a unified open science environment bridging data and software lifecycles across disciplines, from proposal to publication

Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements hinder adoption. Existing approaches rarely enable researchers to keep using their preferred tools or support seamless execution across domains. To close this gap, we developed the open-source Reproducible Research Platform (RRP), which unifies research data management with version-controlled, containerized computational environments in modular, shareable projects. RRP enables anyone to execute, reuse, and publish fully documented, FAIR research workflows without manual retrieval or platform-specific setup. We demonstrate RRP's impact by reproducing results from diverse published studies, including work over a decade old, showing sustained reproducibility and usability. With a minimal graphical interface focused on core tasks, modular tool installation, and compatibility with institutional servers or local computers, RRP makes reproducible science broadly accessible across scientific domains.

cs.DL↗

arXiv2025

Contact cluster modeling of allosteric communication in PDZ domains

Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While it is commonly attributed to conformational rearrangements, the underlying dynamical mechanisms remain poorly understood. The contact cluster model of allostery [J. Chem. Theory Comput. 2024, 20, 10731-10739] identifies localized groups of highly correlated contacts that mediate interactions between secondary structure elements. This framework proposes that allostery proceeds through a multistep process involving cooperative contact changes within clusters and communication between distant clusters, transmitted through rigid secondary structures. To demonstrate the validity and generality of the model, this Perspective employs extensive molecular dynamics simulations ($\sim1\,$ms total simulation time) of four different photoswitchable PDZ domains and studies how different domains, ligands, and perturbations influence both the contact clusters and their dynamical evolution. These analyses reveal several recurring clusters that represent shared flexible structural modules, such as loops connecting $\beta$-sheets, and show that the characteristic time scales of the nonequilibrium protein response can be directly associated with the motions of individual contact clusters. Thus, the dynamic decomposition of PDZ domains into contact clusters uncovers a modular, dynamics-based architecture that underlies and facilitates long-range allosteric communication.

physics.atm-clus↗