Masoud Amiri Farsani

MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary

Dominik Sordyl, Etienne Boileau, Agata Bernat, Satyabrata Maiti et autres

MODOMICS is the reference database of RNA modifications and related information, integrating chemical, biochemical, structural, and functional data. In this 2025 update, marking the 20th anniversary of MODOMICS, the database has been significantly expanded in scope and depth. The RNA sequence section …

pl, de, it, us (code pays fourni par la source)

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 …

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

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

RNA-Puzzles Round V: blind predictions of 23 RNA structures

Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak et autres

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by …

cn, br, Nigéria, pl, us, fr, gb, es, de, cl, be, ru (code pays fourni par la source)

NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids

Elsa Balduzzi, Frédéric Geinguenaud, Dominik Sordyl, Satyabrata Maiti et autres

The Nucleic Acid InfraRed Data Bank (NAIRDB) serves as a comprehensive public repository dedicated to the archival and free distribution of Fourier transform infrared (FTIR) spectral data specific to nucleic acids. This database encompasses a collection of FTIR spectra covering diverse nucleic …

fr, pl (code pays fourni par la source)

SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories

S Naeim Moafinejad, Belisa R. H. de Aquino, M. Boniecki, Iswarya P. N. Pandaranadar Jeyeram et autres

Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform for RNA 3D structure prediction and analysis of RNA folding …

pl, us (code pays fourni par la source)

RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints

Eugene F. Baulin, Sunandan Mukherjee, S Naeim Moafinejad, Tomasz K. Wirecki et autres

Ribonucleic acid (RNA) molecules serve as master regulators of cells by encoding their biological function in the ribonucleotide sequence, particularly their ability to interact with other molecules. To understand how RNA molecules perform their biological tasks and to design new sequences with …

pl (code pays fourni par la source)