Related papers: Integrating Coarse-Grained Simulations and Deep Le…

DDX3X is a human DEAD-box RNA helicase implicated in many cancers and in viral progression. In addition to the RecA-like catalytic core, DDX3X contains N- and C-terminal domains. Here, we investigate the substrate and protein requirements…

Helicases are molecular motors that unwind double-stranded nucleic acids (dsNA), such as DNA and RNA). Typically a helicase translocates along one of the NA single strands while unwinding and uses adenosine triphosphate (ATP) hydrolysis as…

Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism…

The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…

Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…

Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited…

Deep neural networks (DNNs) have achieved extraordinary success in numerous areas. However, to attain this success, DNNs often carry a large number of weight parameters, leading to heavy costs of memory and computation resources.…

Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA).…

Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…

Training deep neural networks is a very demanding task, especially challenging is how to adapt architectures to improve the performance of trained models. We can find that sometimes, shallow networks generalize better than deep networks,…

Deep unrolling, or unfolding, is an emerging learning-to-optimize method that unrolls a truncated iterative algorithm in the layers of a trainable neural network. However, the convergence guarantees and generalizability of the unrolled…

This paper investigates the deep learning optimization problem with softmax cross-entropy loss. We propose a layer separation strategy to alleviate the strong nonconvexity encountered during training deep networks. For cross-entropy models…

Synthesis and efficient implementation mRNA strands has been shown to have wide utility, especially recently in the development of COVID vaccines. However, the intrinsic chemical stability of mRNA poses a challenge due to the presence of…

DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…

The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…

Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…

Differential Diagnosis (DDx) is the process of identifying the most likely medical condition among the possible pathologies through the process of elimination based on evidence. An automated process that narrows a large set of pathologies…

Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…

Pruning Deep Neural Networks (DNNs) is a prominent field of study in the goal of inference runtime acceleration. In this paper, we introduce a novel data-free pruning protocol RED++. Only requiring a trained neural network, and not specific…

In molecular dynamics (MD), neural network (NN) potentials trained bottom-up on quantum mechanical data have seen tremendous success recently. Top-down approaches that learn NN potentials directly from experimental data have received less…