Abstract Motivation: Systematic dissection of the ubiquitylation proteome is emerging as an appealing but challenging research topic because significant roles play not only in protein degradation also many other cellular functions. High-throughput experimental studies using mass spectrometry have identified sites, primarily from eukaryotes. However, vast majority sites remain undiscovered, even well-studied systems. Because spectrometry–based approaches for identifying events are costly,...

The early determination of family for a newly found enzyme molecule becomes important because it is directly related to the detail information about which specific target acts on, as well its catalytic process and biological function. Unfortunately, still hard work distinguish classes by experiments. With an enormous amount protein sequences uncovered in genome research, both challenging indispensable develop automatic method fast reliably classifying family. Using concept Chou's pseudo...

In vivo, some proteins exist as monomers and others oligomers. Oligomers can be further classified into homo-oligomers (formed by identical subunits) hetero-oligomers different subunits), they form the structural components of various biological functions, including cooperative effects, allosteric mechanism ion-channel gating. Therefore, with avalanche protein sequences generated in post-genomic era, it is very important for both basic research pharmaceutical industry to acquire possible...

Protein methylation is predominantly found on lysine and arginine residues, carries many important biological functions, including gene regulation signal transduction. Given their involvement in expression, protein regulatory enzymes are implicated a variety of human disease states such as cancer, coronary heart neurodegenerative disorders. Thus, identification sites can be very helpful for the drug designs various related diseases. In this study, we developed method called PMeS to improve...

Post-translational lysine methylation and acetylation are two major modifications of residues. They play critical roles in various biological processes, especially gene regulation. Identification protein sites would be a foundation for understanding their modification dynamics molecular mechanism. This work presents method called PLMLA that incorporates sequence information, secondary structure amino acid properties to predict residues whole sequences. We apply an encoding scheme based on...

We present a mutual compensation scheme of three phase fluctuations, originating from the residual amplitude modulation (RAM) in process, bright squeezed light generation system. The influence RAM on each locking loop is harmonized by using one electro-optic modulator (EOM), and direction fluctuation manipulated positioning photodetector (PD) that extracts error signal before or after optical parametric amplifier (OPA). Therefore with non-classical noise reduction π obtained. By fitting...

Abstract As one of the most important reversible types post-translational modification, protein methylation catalyzed by methyltransferases carries many pivotal biological functions as well essential processes. Identification sites is prerequisite for decoding regulatory networks in living cells and understanding their physiological roles. Experimental methods are limitations labor-intensive time-consuming. While silicon approaches cost-effective high-throughput manner to predict potential...

Protein glycation is a familiar post-translational modification (PTM) which two-step non-enzymatic reaction. Glycation not only impairs the function but also changes characteristics of proteins so that it related to many human diseases. It still much more difficult systematically detect sites due glycated residues without crucial patterns. Computational approaches, can filter supposed prior experimental verification, extremely increase efficiency experiment work. However, previous lysine...

Channel multiplexing quantum communication based on exploiting continuous-variable entanglement of optical modes offers great potential to enhance channel capacity and save resource. Here, we present a frequency-comb-type control scheme for simultaneously extracting lot entangled sideband with arbitrary frequency detuning from squeezed state light. We experimentally demonstrate fourfold dense coding by the extracted four pairs modes. Due high wide separation between each pairs, these...

Protein lysine acetylation is a type of reversible post-translational modification that plays vital role in many cellular processes, such as transcriptional regulation, apoptosis and cytokine signaling. To fully decipher the molecular mechanisms acetylation-related biological an initial but crucial step recognition acetylated substrates corresponding sites. In this study, we developed position-specific method named PSKAcePred for prediction based on support vector machines. The residues...

Abstract Summary: Lysine succinylation orchestrates a variety of biological processes. Annotation in proteomes is the first-crucial step to decipher physiological roles implicated pathological In this work, we developed novel site online prediction tool, called SuccFind, which constructed predict lysine sites based on two major categories characteristics: sequence-derived features and evolutionary-derived information sequence via an enhanced feature strategy for further optimizations. The...

Abstract Motivation Protein malonylation is a novel post-translational modification (PTM) which orchestrates variety of biological processes. Annotation in proteomics the first-crucial step to decipher its physiological roles are implicated pathological Comparing with expensive and laborious experimental research, computational prediction can provide an accurate effective approach identification many types PTMs sites. However, there still no online predictor for lysine malonylation. Results...

We report on a high-level squeezed vacuum state with maximum quantum noise reduction of 13.2 dB directly detected at the pump power 180 mW. The dependence squeezing factor is experimentally exhibited. When considering only loss and phase fluctuation, fitting results have large deviation from measurement value near threshold. By integrating green-light-induced infrared absorption (GLIIRA) loss, can be perfectly fitted in whole range. result indicates that GLIIRA should thoroughly considered...

Lysine acetylation exists extensively in prokaryotes, and plays a vital role function adjustment. Recent progresses the identification of prokaryote substrates sites provide great opportunity to explore difference substrate site specificity between prokaryotic eukaryotic acetylation. Motif analysis suggests that have distinct location-specific difference, it is necessary develop prokaryote-specific prediction tool.Therefore, we collected nine species lysine data from various databases...

Abstract Motivation Accurately predicting the drug-target binding affinity (DTA) is crucial to drug discovery and repurposing. Although deep learning has been widely used in this field, it still faces challenges with insufficient generalization performance, inadequate use of three-dimensional (3D) information poor interpretability. Results To alleviate these problems, we developed PocketDTA model. This model enhances performance by pre-trained models ESM-2 GraphMVP. It ingeniously handles...

Laser intensity noise is a main limitation of measurement and sensing mission represented by gravitational wave detection. We develop decomposition model design the core elements feedback loop independently based on analysis results. construct fiber amplifier system with ultra-low in 0.1 mHz-1 Hz frequency band employment an optoelectronic that specially designed. The study provides experimental basis technologies for precise at frequency.

Protein phosphorylation catalysed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of kinase-specific sites and disease-related substrates that have been identified, desire to explore relationship between protein is motivated. In this work, we analysed kinases' characteristic all using our developed Phosphorylation Set Enrichment Analysis (PSEA) method. We evaluated efficiency method with independent test concluded approach reliable...