Related papers: Proofreading through spatial gradients
In this article, we derive the limit of detection for a two-step molecular recognition process and show that in-spite of all the recognition reactions being in equilibrium the overall error rates can be reduced exactly as much as possible…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodellers and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed…
Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties. The emergence of deep learning methods for…
Accelerated proximal gradient methods have recently been developed for solving quasi-static incremental problems of elastoplastic analysis with some different yield criteria. It has been demonstrated through numerical experiments that these…
Fine-tuning over large pretrained language models (PLMs) has established many state-of-the-art results. Despite its superior performance, such fine-tuning can be unstable, resulting in significant variance in performance and potential risks…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…
A core challenge in structural biophysics is generating biomolecular conformations that are both physically plausible and consistent with experimental measurements. While sequence-to-structure diffusion models provide powerful priors,…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
Enzymes are biological catalysts that can accelerate chemical reactions compared to uncatalyzed reactions in aqueous environments. Their catalytic efficiency is quantified by the turnover number (kcat), a parameter in enzyme kinetics.…
A recently experimentally observed biochemical "threshold filtering" mechanism by processes catalyzed by the enzyme malate dehydrogenase is explained in terms of a model that incorporates an unusual mechanism of inhibition of this enzyme…
In the realm of image synthesis, achieving fidelity to a reference image while adhering to conditional prompts remains a significant challenge. This paper proposes a novel approach that integrates a diffusion model with latent space…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Identifying enzymes that catalyze target biochemical reactions is a key step in computational enzyme discovery and biocatalyst design. Recent representation-learning methods formulate this problem as enzyme--reaction matching, where paired…
As the field of deep learning steadily transitions from the realm of academic research to practical application, the significance of self-supervised pretraining methods has become increasingly prominent. These methods, particularly in the…
Recent quantum algorithms pertaining to electronic structure theory primarily focus on threshold-based dynamic construction of ansatz by selectively including important many-body operators. These methods can be made systematically more…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
The process of differential deposition is currently applied at the ESRF in order to correct figure errors of x-ray optics substrates, prior to multilayer deposition. The substrate is moved at a controlled speed in front of a sputtering…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…