Attempt to predict predicts protein structure tertiary. Medical search. Frequent questions

The idea of abstract shapes has long been used to characterize different types of structures. (biomedcentral.com)
In silico studies of protein flexibility have attempted to characterize and predict flexible regions based on simple principles. (rostlab.org)

Accurate secondary structure prediction provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs. (biomedcentral.com)
Our approach was applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots. (biomedcentral.com)
Many types of ncRNAs perform their functions through both their sequences and secondary structures, which are defined by the interacting base pairs. (biomedcentral.com)
Of the characterized secondary structures of ncRNAs, Watson-Crick (C-G and A-U) and wobble base p airs (G-U) are most commonly seen. (biomedcentral.com)
As knowing the secondary structure provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs, deriving the secondary structures of ncRNAs remains an important research topic in RNA informatics. (biomedcentral.com)
Pseudoknot is an important structural motif in secondary structures of many types of ncRNAs. (biomedcentral.com)
Although there is promising progress, finding the native secondary structure is still difficult. (biomedcentral.com)
Predicting the minimum free energy secondary structure that includes pseudoknots has been proven to be NP-hard [ 8 ]. (biomedcentral.com)
The system uses both global and local information (i.e., features from the entire protein such as secondary structure composition, protein length, and fraction of surface residues, and features from a local window of sequence-consecutive residues). (rostlab.org)
In addition to angles, we make use of sequence properties like secondary structure at each time-step, without using any database. (sciencegate.app)

It is recently shown that using the abstract shapes, which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions, can improve the performance of structure prediction. (biomedcentral.com)
In this work, we use SVM-based feature selection to derive the consensus abstract shape of homologous ncRNAs and apply the predicted shape to structure prediction including pseudoknots. (biomedcentral.com)
Using predicted shapes in structure prediction allows us to achieve approximate 29% higher sensitivity and 10% higher positive predictive value than other pseudoknot prediction tools. (biomedcentral.com)
The combination of mass data analysis and SVM-based feature selection makes our approach a promising method for shape and structure prediction. (biomedcentral.com)
With advances in sequencing technologies and structure prediction, more pseudoknot structures are expected to be disclosed. (biomedcentral.com)
The predicted shape will then be used to guide structure prediction. (biomedcentral.com)
How to use model quality assessment to further improve the accuracy of protein structure prediction, especially not reliant on the existing templates, is helpful for unraveling the folding mechanism. (sciencegate.app)
Here, we investigate whether model quality assessment can be introduced into structure prediction to form a closed-loop feedback, and iteratively improve the accuracy of de novo protein structure prediction. (sciencegate.app)
Results: In this study, we propose a de novo protein structure prediction method called RocketX. (sciencegate.app)
AbstractQuality Assessment (QA) plays an important role in protein structure prediction. (sciencegate.app)
Our experiment points out new directions for QA problem and our method could be widely used for protein structure prediction problem. (sciencegate.app)
The NMR-assisted modeling challenge in CASP13 provided a blind test to explore the capabilities and limitations of current modeling techniques in leveraging NMR data which had high sparsity, ambiguity and error rate for protein structure prediction. (sciencegate.app)
Here, using atomistic molecular dynamics simulation, we study the correlations between the RBD dynamics with physically distant residues in the spike protein, and provide a deeper understanding of their role in the infection, including the prediction of important mutations and of distant allosteric binding sites for therapeutics. (biorxiv.org)
In the present report we have compared and contrasted structure- and sequence-based methods of prediction to over 5500 genes carrying nearly 24,000 nsSNPs, by employing an automatic comparative modelling procedure to build models for the genes. (biomedcentral.com)

We used this analysis to develop a neural network-based method that predicts flexible-rigid residues from amino acid sequence. (rostlab.org)
In GeomNet, the co-evolutionary features extracted from MSA that search from the sequence databases are sent to an improved residual neural network to predict the inter-residue geometric constraints. (sciencegate.app)

The most ubiquitous D614G mutation is predicted ab-initio from our model. (biorxiv.org)
Linkage to aryl hydrocarbon-interacting protein gene (AIP) mutation has been identified in some families with prolactinoma and in childhood-onset pituitary adenomas. (medscape.com)

We give examples of mutations in genes that are predicted to be deleterious and may have a role in disease. (biomedcentral.com)
0.001) compared to patients without NI-LGE, with no significant difference in the burden of rare protein altering variants in DCM-associated genes between groups (9.7% vs 6.7%, odds ratio 1.5, 95% CI 0.5-4.4, p=0.41). (imperial.ac.uk)

An LSTM network is used to predict the quality by treating each amino acid as a time-step and consider the final value returned by the LSTM cells. (sciencegate.app)

5 , 7 - 9 More specifically, a study analyzing 10,022 SARS-CoV-2 genomes from 68 countries revealed 2969 different missense variants, with 427 variants in the S protein. (biorxiv.org)
Hence, the discovery of causal variants for common diseases is set to accelerate and it would be advantageous if the functional effects of SNPs could be predicted bioinformatically, in order to direct functional studies and narrow down the best candidate SNPs in regions of the genome that show high LD. (biomedcentral.com)

However, the accuracy of the native structure derivation of ncRNAs is still not satisfactory, especially on sequences containing pseudoknots. (biomedcentral.com)
Extensive analysis of RNA properties based on SVM allows us to identify important properties of sequences and structures related to their shapes. (biomedcentral.com)
A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). (biomedcentral.com)

The third study established that residues in active sites of enzymes are predicted by our method to have unexpectedly low B-values. (rostlab.org)
Our model, based on time-independent component analysis (tICA) and protein graph connectivity network, was able to identify multiple residues, exhibiting long-distance coupling with the RBD opening dynamics. (biorxiv.org)
We applied time-independent component analysis (tICA) and protein connectivity network model, on all-atom molecular dynamics trajectories, to identify key non-RBD residues, playing crucial role in the conformational transition facilitating spike-receptor binding and infection of human cell. (biorxiv.org)

Protein flexibility and rigidity predicted from sequence. (rostlab.org)
The most important local feature was the evolutionary exchange profile reflecting sequence conservation in a family of related proteins. (rostlab.org)
For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. (biomedcentral.com)
The most identifiable category of SNP is the small proportion (less than 1%) that change protein sequence, the most common of which is the non-synonymous SNP. (biomedcentral.com)

It would be an advantage if the functional effects of an nsSNP on protein structure and function could be predicted, both for the final identification process of a causal variant in a disease-associated chromosome region, and in further functional analyses of the nsSNP and its disease-associated protein. (biomedcentral.com)

Many computational methods have been used to determine the native structure of ncRNAs. (biomedcentral.com)
Traditional protein QA methods suffer from searching databases or comparing with other models for making predictions, which usually fail. (sciencegate.app)
AbstractComputational methods that produce accurate protein structure models from limited experimental data, e.g. from nuclear magnetic resonance (NMR) spectroscopy, hold great potential for biomedical research. (sciencegate.app)

6 Significantly, the sites in S protein have been demonstrated to be vulnerable to acquire mutations. (biorxiv.org)
Plasma alanine aminotransferase (ALT), measured at 24-hour intervals from 24-96 hours after dosing and evaluated as the area under the curve (AUC), was significantly lower in the mixture groups than predicted by the sum of measured responses to each chemical alone, indicating a less-than-effect-additive joint toxic action. (cdc.gov)

Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)

Contrary to previous reports, we also show that rare mutations are consistently predicted to be deleterious as often as commonly occurring nsSNPs. (biomedcentral.com)

Therefore, we expect that this method will assist in many attempts at inferring aspects of function. (rostlab.org)
Knowledge of the three dimensional structure of a gene product is of major assistance in predicting and understanding its function, its role within the cell and its role in disease. (biomedcentral.com)
Inverse-variance weighted MR was utilized for analyses on outcomes of atrial fibrillation, coronary artery disease, heart failure, ischaemic stroke, and 16 measures of cardiac structure and function. (imperial.ac.uk)

Results for the binary mixture, presented primarily for the moderate and high dose groups, were compared with those obtained with each chemical alone and with what would be predicted from effect addition. (cdc.gov)

One recent attempt is to first predict the abstract shapes (or shapes for short), which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions [ 9 ]. (biomedcentral.com)
Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)

1 , 2 Largely expressed on the surface of SARS-CoV-2, the spike (S) protein plays a crucial role in binding to the host angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD) and facilitating viral entry, 3 , 4 which is therefore considered as one of the most preferred targets against SARS-CoV-2. (biorxiv.org)

Motivation: The successful application of deep learning has promoted progress in protein model quality assessment. (sciencegate.app)
The structure model is folded based on the predicted geometric constraints. (sciencegate.app)

Globular proteins have been the best studied, being easier to isolate in vitro , separated from other cellular bio-chemical interactions. (creation.com)
Thousands of globular proteins are critically important, and are used as enzymes and for other purposes 8 . (creation.com)
9 To function at all, and reliably, globular proteins must fold into precise three dimensional structures. (creation.com)
It should also be noted that alignment techniques generally require the conservation of whole domains and are tuned for optimal performance on water-soluble globular proteins. (biomedcentral.com)

Contrary to this opinion, it was alleged that protein folds are very common among random amino acid chains. (creation.com)

These disease-associated amyloids have in common that they represent a non-functional and off-pathway misfolding and aggregation event of proteins or protein fragments destabilized from reaching their native structure by mutation, environmental conditions or misprocessing. (nature.com)
However, the most prevalent ab initio models still utilize known protein structures to some degree, i.e. small structural fragments with the strong sequence-structure relationship [ 7 ]. (biomedcentral.com)
As such, structural fragments are used as building blocks in reconstructing the complete structure of the target protein. (biomedcentral.com)

Identifying response to acid suppressive therapy in functional dyspepsia using a random starting day trial�is gastro-oesophageal reflux necessary The usefulness of a structured questionnaire within the evaluation of symptomatic gastroesophageal reflux disease. (dnahelix.com)
The list of proteins shown to form so-called functional amyloid fibers in vivo has greatly expanded over the years, but detailed structural insights have not followed at a similar pace in part due to the associated experimental barriers. (nature.com)
Until now, this problem has been approached using machine learning techniques that attempt to predict membership, or otherwise, to predefined functional categories or subcellular locations. (biomedcentral.com)

High-throughput technologies are helping to provide additional sources of information that can be used to predict protein function, typically through the detection of physical protein-protein interactions, or the analysis of gene expression patterns. (biomedcentral.com)
PMID- 19410251 TI - Association of C-reactive protein (CRP) gene allelic variants with serum CRP levels and hypertension in Turkish adults. (nih.gov)
Linkage to aryl hydrocarbon-interacting protein gene (AIP) mutation has been identified in some families with prolactinoma and in childhood-onset pituitary adenomas. (medscape.com)

Computational sequence comparison methods are then typically applied to extend these annotations to related proteins from the same or a different organism. (biomedcentral.com)

This would indicate that abiogenesis beginning with proteins in the absence of a genetic code would have no scientific support. (creation.com)

After demonstrating the reconstruction potential of distance maps, we develop two classes of predictors using two-dimensional recursive neural networks: an ab initio predictor that relies only on the protein sequence and evolutionary information, and a template-based predictor in which additional structural homology information is provided. (biomedcentral.com)
However, the accuracy of template-based models strongly relies on the degree of similarity between the target and its templates, thus preventing its application to a significant fraction of unannotated proteins. (biomedcentral.com)

In Part 1 we address protein-folding experiments that are based on proteins constructed of very few but specified types of amino acids. (creation.com)
Our experiments on a strictly non-redundant set of eukaryotic proteins reveal that the strongest and most easily detected sequence-to-function relationships are concerned with targeting to various cellular compartments, which is an area already well studied both experimentally and computationally. (biomedcentral.com)
Accurate descriptions of protein function usually arise through repeated cycles of laboratory experiments and publication, followed by expert annotation by database curators (e.g. (biomedcentral.com)

Although once considered an implausible target for structural biology, recent developments in cryo-electron microscopy (cryoEM) and helical processing have facilitated the structure determination of amyloid fibrils at near atomic resolution 1 . (nature.com)
It is precisely this helical symmetry that has been leveraged with great success in modern cryoEM approaches to resolve the structural details of a wide range of amyloid structures. (nature.com)
However, deciphering this structure-function relationship requires the availability of much more structural data than experimental methods can currently provide. (biomedcentral.com)

They are genetically expressed by mostly higher life-forms for structure but not for the fundamental biochemical processes necessary for life. (creation.com)
The ability to correlate the function of a protein and its three-dimensional (3D) structure is a challenge of fundamental importance in computational biology. (biomedcentral.com)

A polypeptide which produces a single, lowest energy folded structure will not thereby automatically provide any biological value, but such a scaffold is one prerequisite for useful function. (creation.com)

This makes it very difficult to study and characterize membrane proteins in their relevant state. (creation.com)

There also tertiary etc time scales forming a fractal hierarchy coming in powers of p 1/2 and by p-adic length scales as preferred half octaves. (blogspot.com)

TGD provides a model for this state and predicts similar states for muon and tau and evidence also for these states have been found but also forgotten. (blogspot.com)

Membrane proteins probably make up the majority of all proteins found in the cell. (creation.com)

This picture leads to ask whether the p-adic length scale hierarchy predicted by TGD could provide some understanding concerning the period of T=26 seconds associated with the pulsations. (blogspot.com)
Protein inter-residue contact maps provide a translation and rotation invariant topological representation of a protein. (biomedcentral.com)

Results for the binary mixture, presented primarily for the moderate and high dose groups, were compared with those obtained with each chemical alone and with what would be predicted from effect addition. (cdc.gov)
Plasma alanine aminotransferase (ALT), measured at 24-hour intervals from 24-96 hours after dosing and evaluated as the area under the curve (AUC), was significantly lower in the mixture groups than predicted by the sum of measured responses to each chemical alone, indicating a less-than-effect-additive joint toxic action. (cdc.gov)

For bacterial amyloid pathways like curli and Fap, it is clear that accessory proteins ensure a timely and localized amyloid deposition, including chaperone-like safeguards that prevent or stop premature amyloidogenesis 9 , 10 . (nature.com)

Despite differences in proto-fibril architecture and fiber helical symmetry, most amyloid structures share several conserved features that allow us to expand the definition of the amyloid fold beyond the traditional cross-beta adage. (nature.com)

To the best of our knowledge, all currently described amyloid structures consist of a repetitive stacking of intricate, serpentine, planar β-strand arrangements that are stabilized by steric zipper motifs wherein interdigitated residue side chains make extensive Van der Waals, electrostatic, hydrophobic and hydrogen bonding contacts. (nature.com)

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