Related papers: Improvements of the REDCRAFT Software Package
The rate-distortion performance of neural image compression models has exceeded the state-of-the-art for non-learned codecs, but neural codecs are still far from widespread deployment and adoption. The largest obstacle is having efficient…
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
RFdiffusion is a popular and well-established model for generation of protein structures. However, this generative process offers limited insight into its internal representations and how they contribute to the final protein structure.…
Nuclear Magnetic Resonance (NMR) spectroscopy is a central characterization method for molecular structure elucidation, yet interpreting NMR spectra to deduce molecular structures remains challenging due to the complexity of spectral data…
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized,…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
Accurate protein structures are essential for understanding biological function, yet incorporating experimental data into protein generative models remains a major challenge. Most predictors of experimental observables are…
We present a neural network classification (NNC) method for photometric redshift estimation that produces well-calibrated redshift probability density functions (PDFs). The method discretizes the redshift space into ordered bins and…
We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to…
Deep learning has revolutionized computing in many real-world applications, arguably due to its remarkable performance and extreme convenience as an end-to-end solution. However, deep learning models can be costly to train and to use,…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
Recent advances in quantum crystallography have shown that, beyond conventional charge density refinement, a one-electron reduced density matrix (1-RDM) satisfying N-representability conditions can be reconstructed using jointly…
Determining atomic structure from spectroscopic data is central to materials science but remains restricted to a limited set of techniques and material classes, largely due to the computational cost and complexity of structural refinement.…
The technique of non-redundant masking (NRM) transforms a conventional telescope into an interferometric array. In practice, this provides a much better constrained point spread function than a filled aperture and thus higher resolution…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
Remarkable progress has been made in 3D reconstruction from single-view RGB-D inputs. MCC is the current state-of-the-art method in this field, which achieves unprecedented success by combining vision Transformers with large-scale training.…