Variable resolution configuration is a defining feature of the NCAR MPAS (Model for Prediction Across Scales) model, which allows us to smoothly vary the horizontal resolution for taking a closer look at an area of interest. In this study, we aimed t...
Intrinsically disordered regions (IDRs) carry out many cellular functions and vary in length and placement in protein sequences. This diversity leads to variations in the underlying compositional biases, which were demonstrated for the short vs. long...
Disorder prediction methods that can discriminate between ordered and disordered regions have contributed fundamentally to our understanding of the properties and prevalence of intrinsically disordered proteins (IDPs) in proteomes as well as their fu...
Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of prote...
Intrinsically Disordered Proteins (IDPs) and Regions (IDRs) exist widely. Although without well-defined structures, they participate in many important biological processes. In addition, they are also widely related to human diseases and have become p...
AlphaFold2 (AF2) is a protein structure prediction program which provides accurate models. In addition to predicting structural domains, AF2 assigns intrinsically disordered regions (IDRs) by identifying regions with low prediction reliability (pLDDT...
We used fuzzy entropy as a feature to optimize the intrinsically disordered protein prediction scheme. The optimization scheme requires computing only five features for each residue of a protein sequence, that is, the Shannon entropy, topological ent...
The natively unfolded nature of intrinsically disordered proteins (IDPs) relies on several physicochemical principles, of which the balance between a low sequence hydrophobicity and a high net charge appears to be critical. Under this premise, it is...
Conformational protein properties are coupled to protein functionality and could provide a useful parameter for functional annotation of differentially expressed genes in transcriptome studies. The aim was to determine whether predicted intrinsic pro...
With over 60 disorder predictors, users need help navigating the predictor selection task. We review 28 surveys of disorder predictors, showing that only 11 include assessment of predictive performance. We identify and address a few drawbacks of thes...
Driven by the variety of available measures intended to estimate predictability of diverse objects such as time series and network links, this paper presents a comprehensive overview of the existing literature in this domain. Our overview delves into...
Obtaining accurate forecasts for the evolution of epidemic outbreaks from deterministic compartmental models represents a major theoretical challenge. Recently, it has been shown that these models typically exhibit trajectory degeneracy, as different...
To determine whether (or not) the intrinsic predictability limit of the atmosphere is two weeks and whether (or not) Lorenz’s approaches support this limit, this entry discusses the following topics: (A). The Lorenz 1963 model qualitatively rev...
Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and pla...
Disordered linkers (DLs) are intrinsically disordered regions that facilitate movement between adjacent functional regions/domains, contributing to many key cellular functions. The recently completed second Critical Assessments of protein Intrinsic D...
Identification of intrinsic disorder in proteins and proteomes has revealed important novel aspects of protein function and interactions. However, it has been pointed out that several oligomeric fibrillar protein motifs such as coiled coils and colla...
Protein tandem repeats (TRs) are often associated with immunity-related functions and diseases. Since that last census of protein TRs in 1999, the number of curated proteins increased more than seven-fold and new TR prediction methods were published....
The cost of next-generation sequencing technologies is rapidly declining, making RNA-seq-based gene expression profiling (GEP) an affordable technique for predicting receptor expression status and intrinsic subtypes in breast cancer patients. Based o...
The quick, simultaneous movements of both eyes in the same direction is called a saccade, and the process of developing an internal model for the eyes’ movement-control based on visual stimuli is called saccade learning. All humans use this typ...
Intrinsic disorder is very important in the biological function of several proteins, and is directly linked to their foldability during interaction with their targets. There is a close relationship between the intrinsically disordered proteins and th...
Alpha-synuclein is a key protein involved in the development and progression of Parkinson’s disease and other synucleinopathies. The intrinsically disordered nature of alpha-synuclein hinders the computational screening of new drug candidates f...
Intrinsically disordered proteins or protein regions are involved in key biological processes including regulation of transcription, signal transduction, and alternative splicing. Accurately predicting order/disorder regions ab initio from the protei...
Second-order damping oscillation models are incapable of precisely predicting superimposed and multi-fruit collision-induced oscillations. In view of this problem, an ARIMA-EEMD-LSTM hybrid model for predicting the oscillation trajectories of trellis...
Grinding, as the most crucial finishing process for bearing rings, influences the surface integrity of bearings through the roughness of the ground surface. In order to improve the surface roughness of bearing ring grinding under multiple working con...
Intrinsic radiosensitivity is a major determinant of radiation response. Despite the extensive amount of radiobiological data available, variability among different studies makes it very difficult to produce high-quality radiosensitivity biomarkers o...
Whereas the concept of intrinsic disorder derives from biophysical observations of the lack of structure of proteins or protein regions under native conditions, many of our respective concepts rest on proteome-scale bioinformatics predictions. It is...
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of polysaccharides and are today divided into eight families (AA9–11, AA13–17) within...
Ramonda serbica Panc. is an ancient resurrection plant able to survive a long desiccation period and recover metabolic functions upon watering. The accumulation of protective late embryogenesis abundant proteins (LEAPs) is a desiccation tolerance hal...
Operators of industrial machinery relentlessly pursue improving safety, increasing productivity, and minimizing unplanned downtime. Elastomer seals are ubiquitous components of this machinery. In general, static seals are designed to be compressed at...
This paper describes CAREUP, a novel older adult healthy aging support platform based on Intrinsic Capacity (IC) monitoring. Besides standard functionalities like storing health measurement data or providing users with personalized recommendations, t...
Intrinsically disordered proteins perform a variety of important biological functions, which makes their accurate prediction useful for a wide range of applications. We develop a scheme for predicting intrinsically disordered proteins by employing 35...
Objective: Intrinsic capacity is recognized as an important determinant of healthy aging and well-being of older adults; however, relatively little is known about the intrinsic capacity of older adults to predict adverse health outcomes. The study ai...
Reconstituted clays have often provided the basis for the interpretation and modelling of the properties of natural clays. The term “intrinsic” was introduced to describe a clay remoulded or reconstituted at moisture content up to 1.5 tim...
This comprehensive review examines FINCHES (Force field-based Interaction Network for Characterizing Heterotypic and Entropic Sequences). This groundbreaking computational framework enables the rapid, sequence-based prediction of intermolecular inter...
This study explores the role of intrinsically disordered regions (IDRs) in the SARS-CoV-2 proteome and their potential as targets for small-molecule drug discovery. Experimentally validated intrinsic disordered regions from the literature were utiliz...
This work introduces a novel application for predicting the macroscopic intrinsic permeability tensor in deformable porous media, using a limited set of μ-CT images of real microgeometries. The primary goal is to develop an efficient, machine lear...
O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM) to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylate...
Prediction of intrinsic disordered proteins is a hot area in the field of bio-information. Due to the high cost of evaluating the disordered regions of protein sequences using experimental methods, we used a low-complexity prediction scheme. Sequence...
Machine learning (ML) approaches are receiving increasing attention from pharmaceutical companies and regulatory agencies, given their ability to mine knowledge from available data. In drug discovery, for example, they are employed in quantitative st...
This scientific study aims to validate the applicability of a micromechanical model for predicting the static shear strength of hybrid interfaces that are pressure-reinforced and bonded with anaerobic adhesives. To identify the parameters for the mic...
Currently, we assist the emergence of sensors and low-cost information and communication technologies applied to food products, in order to improve food safety and quality along the food chain. Thus, it is relevant to implement predictive mathematica...
Intrinsically disordered proteins and protein regions (IDPs/IDPRs) are mainly involved in signaling pathways, where fast regulation, temporal interactions, promiscuous interactions, and assemblies of structurally diverse components including membrane...
Dysfunctional brain networks have been found in patients with major depressive disorder (MDD). In this study, to verify this in a more straightforward way, we investigated the intrinsic organization of brain networks in MDD by leveraging the resting-...
The functional processes of many proteins involve the association of their intrinsically disordered regions (IDRs) with acidic membranes. We have identified the membrane-association characteristics of IDRs using extensive molecular dynamics (MD) simu...
There is increasing evidence that many intrinsically disordered regions (IDRs) in proteins play key functional roles through interactions with other proteins or nucleic acids. These interactions often exhibit a context-dependent structural behavior....
Background: Breast cancer is intrinsically heterogeneous and is commonly classified into four main subtypes associated with distinct biological features and clinical outcomes. However, currently available data resources and methods are limited in ide...
The basic helix–loop–helix/Per-ARNT-SIM (bHLH-PAS) proteins are a family of transcription factors regulating expression of a wide range of genes involved in different functions, ranging from differentiation and development control by oxygen and toxin...
Mitogen-activated protein kinase (MAPK) inhibition with the combination of BRAF (Rapidly Accelerated Fibrosarcoma) and MEK (Mitogen-activated protein kinase kinase) inhibitors has become the standard of first-line therapy of metastatic melanoma harbo...
Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-...
Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins. Although predictors of disorder have been shown to achieve relatively high rates of correct classification of these se...
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