Protein sequence similarities. Medical search. Frequent questions

One key element in understanding the molecular machinery of the cell is to understand the meaning, or function, of each protein encoded in the genome. (columbia.edu)
BACKGROUND:The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. (novartis.com)
In Part I , we looked at the NCBI SeqViewer, and found a new way to check out a genome map, and learn more about individual genes and proteins. (scienceblogs.com)
To use Blink, I found a record for mumps in the NCBI genome database and selected the Sequence Viewer link (see part I for instructions). (scienceblogs.com)
I liked this method because I could see all the proteins encoded by the mumps genome in one view and look at them one by one. (scienceblogs.com)
This record told me that the mumps nucleocapsid protein, NP_054707.1, protects the viral RNA genome, along with some other information about the structure of the protein. (scienceblogs.com)
Paste in a query sequence to find its location in the the genome. (ucsc.edu)
The high diversity and relatively small genome sizes of these phages provide an ideal platform for introducing high school and undergraduate students to the research laboratory, isolating and naming novel viruses, and determining their genomic sequences. (wikiversity.org)
To search for sequence similarities to the Mycobacterium phage L5 genome, click on the "GenBank: Z18946" link in the GenBank summary page for phage L5 (see Figure 3). (wikiversity.org)
We're now dealing with the amount of data that astrophysicists deal with, all because of the genome sequencing revolution," said ORNL researcher Ada Sedova. (eurekalert.org)
They have modeled the full proteomes - all the proteins coded in an organism's genome - for four microbes, each with approximately 5,000 proteins. (eurekalert.org)
Whole genome sequencing was attempted for specimens with cycle threshold values <30. (cdc.gov)
BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. (cdc.gov)
Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. (cdc.gov)

I'm aware that parsing results from pairwise alignments of all pairwise combinations of proteins from the input file and arranging it into a table is one solution but I'm trying to avoid this at this point as it would take me, with my current skills, a lot of time to write such a script. (biostars.org)
It may miss more divergent or shorter sequence alignments. (ucsc.edu)
For comparisons of proteins with limited sequence and backbone-fold similarity, where coordinate-based methods typically fail, ZEAL can often find alignments with substantial surface-shape correspondence. (lu.se)
If you click on part of the graphical representation of the Che12 sequence, you will move down the page where detailed sequence alignments are shown and it says "3150/3562 (88%)" indicating that for 3562 nucleotides of similar sequences in L5 and Che12 there is 88% sequence identity. (wikiversity.org)
This option can be unchecked for aligning of sequences that are not expected to share conserved domains and are expected to have very short pair wise local alignments. (nih.gov)
Sequence alignments identified that prosaposin-like proteins are ubiquitous in plant kingdom. (umd.edu)

Markov Clustering (MCL) is a popular algorithm for clustering networks in bioinformatics such as protein-protein interaction networks and protein similarity networks. (sciweavers.org)
The bioinformatics tools include those for analyzing 2D-GEL patterns, protein modeling, and protein identification. (nhbs.com)
Objective: The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. (cdc.gov)
This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. (cdc.gov)

Scientists can see the interactions between millions of genes and proteins, speeding up research and treatment of diseases. (infoq.com)

We applied both human monoclonal anti-SARS-Cov-2 antibodies (spike protein, nucleoprotein) and rabbit polyclonal anti-SARS-Cov-2 antibodies (envelope protein, membrane protein) to 55 different tissue antigens. (frontiersin.org)
The next protein is M, or membrane protein. (scienceblogs.com)
If we click Metazoa , we see which metazoan sequence is matching our mysterious membrane protein. (scienceblogs.com)
The H4A3 monoclonal antibody specifically binds to CD107a which is also known as Lysosomal-associated membrane protein 1 (LAMP-1). (bdbiosciences.com)
Lectures dealing with methods for theoretical modelling of membrane protein structure, fusion protein techniques, X-ray crystallography, heterologous expression, solubilisation and purification of membrane proteins are also included in the course. (lu.se)
This is followed by experimental determination using genetic construction and expression of a fusion protein of the membrane protein and a marker protein in a bacterial system which is subsequently analysed. (lu.se)
An individually planned and executed minor project during two weeks, in which the students express a membrane protein of their choice and demonstrate in some way that the expression was successful. (lu.se)

The resulting algorithm, when tested on its ability to recognize previously unseen families from the SCOP database, yields significantly better remote protein homology detection than SVM-Fisher, profile HMMs and PSI-BLAST. (columbia.edu)
The distance metric is the probability that a pair of protein sequences are of the same Interpro family/domain, which facilitates the modelling of transitive homology closure to detect remote homologues. (novartis.com)
We also did selective epitope mapping using BLAST and showed similarities and homology between spike, nucleoprotein, and many other SARS-CoV-2 proteins with the human tissue antigens mitochondria M2, F-actin and TPO. (frontiersin.org)
Cross-reactivity occurs when amino acid sequence homology exists between a pathogen and self-tissue proteins ( 1 ). (frontiersin.org)
Polycystin-L2 has significant homology with polycystins-L and -2, with similarities of 58 and 59%, respectively. (nih.gov)
It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN. (bvsalud.org)

We identify several categories of protein functions where global shape similarity is significantly more likely than expected by random chance, when comparing proteins with little similarity on the fold level. (lu.se)
In particular, we find that global surface shape similarity is particular common among DNA binding proteins. (lu.se)
The degree of 3-dimensional shape similarity between proteins. (bvsalud.org)

A search allows scientists to infer the function of a sequence from similar sequences. (nih.gov)
The megaBLAST nucleotide-nucleotide search, optimized for very similar sequences (in the same or in closely related species), first looks for an exact match of 28 bases, and then attempts to extend that initial match into a full alignment ( 3 , 4 ). (nih.gov)
Reduce computation time by using clusters of similar sequences. (nih.gov)
The idea behind using clusters is that constraints do not contribute information for alignment of very similar sequences. (nih.gov)
Clusters of similar sequences are found using alignment-free k-mer counting-based method. (nih.gov)

These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. (wikipedia.org)
The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
Yan and his coworkers 11 trained a Naïve Bayes classifier by using only sequence information, such as the identities of the target residue and its sequence neighboring residues. (nature.com)
This distance overestimates exponentially scaled percentage of different residues in aligned sequences (see graphs in the above paper for details). (nih.gov)
Sequence analysis predicts that the mouse and human polycystin-L2 proteins consist of 621 and 624 amino acid residues, respectively. (nih.gov)
For sequences with a typical fraction of hydrophobic residues, we impact on how permissive with respect to sequence specificity find that the nonrandomness can be interpreted as anticorrela- the protein folding process is-- only sequences with nonran- tions. (lu.se)

This gene encodes a secreted protein that has low sequence similarity to the dickkopf-3 protein. (nih.gov)
ALMS1 encodes a ~ 0.5 megadalton protein that localises to the base of centrioles. (springer.com)
report the molecular cloning of Painting of fourth (Pof), which encodes a protein that specifically paints chromosome 4 (Proc Natl Acad Sci USA 2001, 98:6273-6278). (the-scientist.com)
[ 4 ] The emm gene encodes the M protein. (medscape.com)

When protein sequences, either confirmed or predicted, enter GenBank, the NCBI has an automated system that uses blastp to compare these sequences to all of the sequences in the protein sequence databases. (scienceblogs.com)
BLASTP performs protein-protein sequence comparison, and its algorithm is the basis of many other types of BLAST searches such as BLASTX and TBLASTN . (nih.gov)
COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. (nih.gov)

Full-length cDNA sequences for both mouse and human polycystin-L2 were obtained from testis cDNA. (nih.gov)

Another practical question is related to genomic sequence inhomogeneity at interspecies level: if GeneMark has not been trained for a particular species, is it possible to apply models derived for phylogenetically close genomes? (aaai.org)
You can use the number (15859) with the BLAST tool to search for other known sequences that are similar to the L5 genomic sequence. (wikiversity.org)

Phylip uses its own special interleaved sequence alignment, which is definitely neither FASTA format nor CLUSTAL format, but you can find programs that will convert. (biostars.org)

Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
For others, which we call "pioneer genes", no significant similarity has been found at a protein sequence level although the confidence of GeneMark prediction is high. (aaai.org)
The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysi. (sciweavers.org)
The Protein Structure Prediction Center announced that AlphaFold2, an AI system developed by DeepMind, has solved its Protein Structure Prediction challenge. (infoq.com)
Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
Wei2GO: weighted sequence similarity-based protein function prediction. (bvsalud.org)
PON-Diso a machine learning based prediction method to predict changes in disorder regions contained in a protein, caused by amino acid substitutions. (lu.se)
Prediction of Protein Stability Changes is a structure-based method to predict the effects of missense variants on protein stability. (lu.se)

This distance metric is based on the pairwise sequence similarity score and the similarity between their domain structures. (novartis.com)
For example, if you just want to see protein sequences that are in 3-D structures, you can do that. (scienceblogs.com)
Results: We present ZEAL, an interactive tool to superpose global and local protein structures based on their shape resemblance using 3D (Zernike-Canterakis) functions to represent the molecular surface. (lu.se)
In response to immune induction, uORF-inhibition is alleviated by three Ded1p/DDX3X-homologous RNA helicases which unwind the RNA structures, allowing ribosomes to bypass the inhibitory uORFs and upregulate defence protein production. (biorxiv.org)
It has been proposed that ribosome scanning and start codon selection are regulated by elements in the 5' leader sequence, such as RNA primary sequences (for example, the Kozak sequence context), upstream open reading frames (uORFs), secondary structures, and RNA modifications 4 - 7 . (biorxiv.org)
A team of scientists led by the Department of Energy's Oak Ridge National Laboratory and the Georgia Institute of Technology is using supercomputing and revolutionary deep learning tools to predict the structures and roles of thousands of proteins with unknown functions. (eurekalert.org)
Researchers are using the Summit supercomputer at ORNL and tools developed by Google's DeepMind and Georgia Tech to speed the accurate identification of protein structures and functions across the entire genomes of organisms. (eurekalert.org)
Because of the need for extensive experimental work to determine three dimensional structures, scientists have only solved the structures for about 170,000 of those proteins. (eurekalert.org)
Being able to see the structures of proteins adds another layer that can help scientists home in on the most promising gene candidates for experiments. (eurekalert.org)
A longstanding effort to do so is by exploiting protein structures to predict new reagents and therapeutic leads (structure-based ligand discovery). (ucsf.edu)
This model, hereafter formation of three-dimensional protein structures. (lu.se)

Both methods yield antibody in solution that is free of most other soluble proteins, lipids, etc. (bdbiosciences.com)

The method, SVM-pairwise, uses a pairwise sequence similarity algorithm such as Smith-Waterman in place of the HMM in the SVM-Fisher method. (columbia.edu)
Clustering these sequences into families is one of the first steps to perform comparative studies across several genomes.RESULTS:Here we report a novel clustering algorithm (CLUGEN) that has been used to cluster sequences of experimentally verified and predicted proteins from all sequenced genomes using a novel distance metric which is a neural network score between a pair of protein sequences. (novartis.com)
A Geometric Algorithm to Find Small but Highly Similar 3D Substructures in Proteins. (uni-marburg.de)
The BLAST algorithm is tuned to find these domains or shorter stretches of sequence similarity. (nih.gov)

These shared biochemical, protein sequence and functional similarities suggest the existence of an ancestral annealing mechanism involved in HR. (nature.com)
Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. (nih.gov)

To identify common features shared by transcripts with stress-upregulated translation efficiency (TE-up), we first performed high-resolution ribosome-sequencing in Arabidopsis during pattern-triggered immunity and found that TE-up transcripts are enriched with upstream open reading frames (uORFs). (biorxiv.org)
This structural similarity was supported by glycosylation analyses of Arabidopsis thaliana AtPSAPLIP1 and AtPSAPLIP2. (umd.edu)
In search of the genes that enable sphagnum moss to tolerate rising temperatures, ORNL scientists start by comparing its DNA sequences to the model organism Arabidopsis, a thoroughly investigated plant species in the mustard family. (eurekalert.org)
Even for plants more closely related to Arabidopsis, we don't have a lot of empirical evidence for how these proteins behave. (eurekalert.org)

This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. (wikipedia.org)
Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. (nature.com)
Also, they share a similar protein architecture based on an N-terminal ssDNA binding domain of ~180 amino acids and a C-terminal extension that in the case of RAD52 is required for homologous recombination (HR) through specific protein-protein interactions 6 . (nature.com)
claiming that two homologous chromosomes paired between complementary sequences lead to the formation of a cross-stranded structure that physically links the two component helices. (iucr.org)

And, the P protein shows us that GenBank is missing a spell check function. (scienceblogs.com)
We have documented such unnoticed genes in GenBank sequences for several species. (aaai.org)

An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. (nih.gov)
In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)
Binding sites of other proteins which are similar to the binding site of the target protein can offer hints for possible side effects of a new drug prior to clinical studies. (uni-marburg.de)
The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. (uni-marburg.de)
How to Measure the Similarity Between Protein Ligand-binding Sites. (uni-marburg.de)
Efficient Similarity Retrieval for Protein Binding Sites based on Histogram Comparison. (uni-marburg.de)
The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria. (uni-marburg.de)
Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites. (lu.se)

Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. (nih.gov)
Structure Determination of Human and Murine Beta-Defensins Reveals Structural Conservation in the Absence of Significant Sequence Similarity. (expasy.org)

Generation of syntactically correct and unambiguous names for proteins is a challenging, yet vital task for functional annotation processes. (sciweavers.org)

In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. (nature.com)
Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. (nih.gov)
Each row corresponds to a specific residue and describes the probability of related sequences having that residue at that position. (nih.gov)

Basic data handling of mass spectrometry data for protein identification, assessment of PTMs and determination of amino acid sequences. (lu.se)

Is there an already existing tool to generate a matrix of pairwise protein identities/similarities for an input which consists of multiple protein sequences? (biostars.org)
Gap opening penalty and gap extension penalty for gaps inside of a sequence used in pairwise global alignment in the progressive alignment stage. (nih.gov)
Gap opening penalty and gap extension penalty for gaps at ends of a sequence used in pairwise global alignment in the progressive alignment stage. (nih.gov)

The recent sequencing of other genomes has provided us with a huge amount of auxiliary sequence data which could help in the characterization of the human genes. (novartis.com)

E.coli polyclonal to GST Tag.Posi Tag is a 45 kDa recombinant protein expressed in E.coli. (biotech2012.org)
Analysis of recombinant SGT2 protein purified from yeast cultures deomonsrated the specifiicity of SGT2 for UDP-glucose confiriming its function as a UDP-glucose:solanidine glucosyl transferase. (usda.gov)
Recombinant, full length human protein. (thermofisher.com)

Coding region inhomogeneity, caused by differences in sequence composition between "native" and horizontally transferred genes or between genes expressed at different levels, contributes to the false negative error rate. (aaai.org)
Compare results from different analyses and from an analytical point of view explain differences and similarities. (lu.se)
There are 4 major subfamilies of emm genes, which are defined by sequence differences within the 3' end, encoding the peptidoglycan-spanning domain. (medscape.com)

A very successful means of inferring the function of a previously unannotated protein is via sequence similarity with one or more proteins whose functions are already known. (columbia.edu)
The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines that act as regulators of immune and nervous cells. (wikipedia.org)
First, I can find something about the function of each of the eight mumps proteins. (scienceblogs.com)
As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. (nature.com)
Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
Studies using purified protein produced in yeast cells has confirmed the biochemical function of the SGT2 protein in SGA production as the UDP-glucose:solanidine glucosyl transferase. (usda.gov)
POF complexes may function like the Male Lethal Specific proteins, which regulate dosage-compensation of the X chromosome. (the-scientist.com)
Hydrogen peroxide does not function downstream of salicylic acid in the induction of PR protein expression. (springer.com)
Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. (uni-marburg.de)
Yet, much of biology happens on the surface of proteins, which is why proteins with shared ancestry and similar function often have comparable surface shapes. (lu.se)
In combination with shape-based matching, ZEAL can be used as a general tool to study relationships between shape and protein function. (lu.se)
There are also readily reproducible methods for protein expression profiling, identifying protein-protein interactions, and protein chip technology, as well as a range of newly developed methodologies for determining the structure and function of a protein. (nhbs.com)
Their deep learning-driven approaches infer protein structure and function from DNA sequences, accelerating new discoveries that could inform advances in biotechnology, biosecurity, bioenergy and solutions for environmental pollution and climate change. (eurekalert.org)
There is only so much we can infer about function from comparing the nucleotide sequences with the model. (eurekalert.org)
ß-Microseminoprotein (MSP) is a small and stable protein with unknown function. (lu.se)
Even though the function of MSP is not known it has been found that it binds very strongly to CRISP-3, another protein with an unknown function. (lu.se)
Group discussions about e.g. the similarities/dissimilarities, cloning and overexpression strategies, and structure and function of membrane proteins. (lu.se)

Furthermore to SQSTM1, NBR1 (NBR1 autophagy cargo receptor) proteins serve identical features as pexophagy receptors [28]. (biotech2012.org)
Applying these to G-Protein Coupled Receptors (GPCRs), which are the single largest family of signaling receptors in human cells. (ucsf.edu)
Developing computational methods to relate receptors by the similarity of their ligands, rather than by protein sequence or structure. (ucsf.edu)
The lectures address the three different main types of membrane proteins and associated cellular processes: transport and transporters, signal transduction and receptors, bioenergetics and photosynthetic and respiratory proteins. (lu.se)

This threshold prvents COBALT from forming clusters o unrelated sequences. (nih.gov)

Rapid and transient activation of myelin basic protein kinase in tobacco leaves treated with hairpin from Erwinia amylovora . (springer.com)

These results will broaden our understanding of the protein-lipid interaction in the cell and the biological functions of saposin-like proteins in plant growth and development. (umd.edu)

As opposed to single strand (ss) DNA binding proteins such as SSB and RPA, which protect and occlude ssDNA from recombination, RAD52/Redβ SSAPs promote recombination and share several biochemical similarities. (nature.com)

We sought to determine whether immune reactivity occurs between anti-SARS-CoV-2 protein antibodies and human tissue antigens, and whether molecular mimicry between COVID-19 viral proteins and human tissues could be the cause. (frontiersin.org)
Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
Extensive evidence has revealed that the core clock machinery involves "clock genes" and "clock proteins" functioning as molecular cogs. (bioone.org)
120 credits) in Chemistry and Molecular Biology and compulsory for a degree of Master of Science (120 credits) in Protein Science. (lu.se)
The main aim of the course is to enable students to acquire specialised knowledge and understanding of membrane biochemistry and the molecular structure, topology and functional mechanisms of membrane proteins. (lu.se)
A number of proteins from each process, for which the structure is known, are explored in greater detail in order to highlight the functional molecular mechanisms. (lu.se)

To under- denoted the AB model, consists of chains of two kinds of stand the statistical distribution of hydrophobicity along proteins ``amino acids'' interacting with Lennard-Jones potentials. (lu.se)

Elucidating functions of these proteins advance understanding of signal transduction from plasma membrane into cytosol and between different intracellular membrane compartments. (umd.edu)

Some of protein products of these genes have been characterized by similarity search methods. (aaai.org)
Tissue culture supernatant is purified by either protein A/G or affinity purification methods. (bdbiosciences.com)
Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
METHODS: We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. (cdc.gov)
Determination of the transmembrane topology of a protein starts with a model of the protein based on sequence information and theoretical methods. (lu.se)

POF protein decorates chromosome 4 by spreading out from an initiation site in the proximal region of the chromosome. (the-scientist.com)
This study supports the idea that there are similarities between the chromosome 4 autosome and the X chromosome. (the-scientist.com)
Motor proteins of the conserved kinesin-14 family have important roles in mitotic spindle organization and chromosome segregation. (elifesciences.org)

We found that SARS-CoV-2 antibodies had reactions with 28 out of 55 tissue antigens, representing a diversity of tissue groups that included barrier proteins, gastrointestinal, thyroid and neural tissues, and more. (frontiersin.org)
Sequence similarity to proteins bearing onco-differentiation antigens. (bdbiosciences.com)

This product is an active protein and may elicit a biological response in vivo, handle with caution. (abcam.com)

COBALT is optimized for cases where groups of sequences do match to the same domain (see Query Clustering below). (nih.gov)

It is also rec- important target organ in the safety assessment of drugs and ognized that different types of immune-mediated responses can be triggered by different classes of compounds and that some immune chemicals, as well as protein- or peptide-based products. (cdc.gov)
Make an experimental plan for preparing and analyzing protein and peptide samples using mass spectrometry. (lu.se)
Practical parts including protein and peptide sample preparations, deposition with different techniques and the use of chromatographic separations for complex samples prior to mass spectrometry analysis. (lu.se)
Manual and automated mass spectrometry acquisition of intact protein and peptide mass determination and determination of peptide sequence information. (lu.se)

Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E-SD-EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages. (iucr.org)

VP1 sequences of these isolates revealed a stepwise divergence from the Sabin 1 sequence at a rate of about 1.1% per year. (cdc.gov)
The visualization schemes include graphs for coloured and property charts, identity, similarity and divergence plots as well as visualizations based on physicochemical properties. (lu.se)

permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)

LAMP-1 is a ~110 kDa type I transmembrane protein that is heavily glycosylated and widely expressed by cells primarily on the luminal surface of their lysosomes. (bdbiosciences.com)
Both human and murine polycystin-L2 proteins are predicted to have seven putative transmembrane (TM) domains, and, by comparison with transient receptor potential channels, the six carboxyl-terminal TM domains are likely to constitute an ion channel subunit. (nih.gov)

In this mechanism, antibodies formed against SARS-CoV-2 would also bind to human tissue proteins leading to autoimmune reactivity. (frontiersin.org)
Our Blink results imply that this sequence is human. (scienceblogs.com)
In addition, the expressed protein in the silkworm baculovirus system was used to study the anti-apoptotic effects of SP2 on human umbilical vein ECs (HUVECs) induced by peroxidation. (hindawi.com)
Some studies have suggested a role for this protein in maintaining centriole-nucleated sensory organelles termed primary cilia, and AS is now considered to belong to the growing class of human genetic disorders linked to ciliary dysfunction (ciliopathies). (springer.com)
Sequence analysis showed high similarity between mink and human sequences on corresponding farms. (cdc.gov)
In addition to the 10 cysteines there are only 16 identical amino acids in the proteins from human, rhesus monkey, baboon, pig, rat and mouse. (lu.se)
The tree-dimensional structure of human and porcine MSP are very similar in spite of only a 50 % identity in the amino acid sequences of the two proteins. (lu.se)
This rate is patterns, gene sequencing, immuno- Centre for Disease Prevention and higher than that of severe acute respira- genicity and the animal-human and hu- Control (ECDC) and the National In- tory syndrome coronavirus (SARS), man-human interfaces. (who.int)

Many receptor protein that regulate pexophagy have already been determined. (biotech2012.org)
The third is that this is also the first time to characterize the plant prosaposin-like proteins, which are important in male gametophyte development and provide novel sights on how plants regulate reproductive process. (umd.edu)
The AMER1 gene provides instructions for making a protein found in tissues throughout the body where it helps regulate the Wnt signaling pathway, which is a series of chemical signals that affect the way cells and tissues develop. (medlineplus.gov)

They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
Significant portion of those affect the drug response as well by changing the protein structure and fu. (sciweavers.org)
The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. (sciweavers.org)
Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). (iucr.org)
Meta AI Research recently announced ESMFold, an AI model for predicting protein structure from a sequence of genes. (infoq.com)
The analysis of domain structure of this protein suggested that it might be involved in correct assembly of thecytochrome bcl complex. (researchgate.net)
Motivation: Most protein-structure superimposition tools consider only Cartesian coordinates. (lu.se)
wavelength corresponding to -helix structure, as one might have statistical analysis on the sequences that fold well indicates expected, but also at large wavelengths. (lu.se)

The expressed protein in Escherichia coli was used to generate polyclonal antibodies. (hindawi.com)

COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. (nih.gov)

Protein crystallization is a commonly used technique for protein analysis and subsequent drug design. (sciweavers.org)
Analysis of Membrane Proteins by Two-Dimensional Gels - Michael Fountoulakis, 15. (nhbs.com)
In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. (cdc.gov)

50% identity, which is very high for proteins), the distances go up exponentially, so that a 50% identical sequence might have a distance of PAM70, while a 30% identical sequence could be PAM160, and 20% identity PAM250. (biostars.org)
The Sgt2 nucleic acid sequence is 68% identical to Sgt1 a UDP-galactose:solanidine galactosyl transferase. (usda.gov)

Under stress conditions, such as nutrition depletion 8 , hypoxia 9 , 10 , or pathogen challenge 11 , global translation is reprogrammed, leading to elevated stress-responsive protein production, but repressed growth-related protein synthesis, which is crucial to the survival and adaptation to stress. (biorxiv.org)

Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. (nature.com)
RESULTS: The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. (cdc.gov)

Electrophoretic mobility shift assays detected allele-dependent nuclear protein binding in A549 cells for 8 of 21 variants. (cdc.gov)

By mechanism, DNA annealing proteins are divided into ATPases capable of strand invasion (RecA, RAD51) and single strand annealing proteins (SSAPs) that do not utilize ATP 4 . (nature.com)
Alternative splicing is an important mechanism for increasing protein diversity. (sciweavers.org)

These genes share sequence similarity with the yeast DNA repair protein Rad5. (thermofisher.com)
The mechanisms involved in the stress-induced translation have been investigated for a small number of key transcription factors (for example, yeast general control nondepressible 4 (GCN4) 12 and mammalian activating transcription factor 4 (ATF4) 13 ), whose translation is normally inhibited by the uORFs in the 5' leader sequences of their mRNAs. (biorxiv.org)
In this study, we show that the yeast kinesin-14 Kar3 generates processive movement as a heterodimer with the non-motor proteins Cik1 or Vik1. (elifesciences.org)

There are many ways of performing a sequence similarity search, but probably the most popular method is the "Basic Local Alignment Search Tool" ( BLAST ) ( 1 , 2 ). (nih.gov)
If instead BLAST started out by attempting to align two sequences over their entire lengths (known as a global alignment), fewer similarities would be detected, especially with respect to domains and motifs. (nih.gov)
PSI-BLAST can then search a database of protein sequences with this PSSM. (nih.gov)
RPSBLAST (Reverse-Position-Specific BLAST ) can very quickly search a protein query against a database of PSSMs that were usually produced by PSI-BLAST . (nih.gov)
DELTA- BLAST produces a PSSM with a fast RPSBLAST search of the query , followed by searching this PSSM against a database of protein sequences ( 5 ). (nih.gov)
When the BLAST search is done, you should see a graphical summary of sequence similarity results (Figure 5). (wikiversity.org)
Use RPS-BLAST to find conserved domains in query sequences to guide alignment. (nih.gov)
E-value threshold for accepting BLAST-P hits in pair wise local alignment of input sequences. (nih.gov)
We recommend using this option for aligning BLAST results and whenever a subset of input sequences that share conserved domains is expected. (nih.gov)

The BLASTN nucleotide-nucleotide search looks for more distant sequences. (nih.gov)

The x-ray repair cross-complementing (XRCC) proteins are responsible for efficiently repairing and maintaining genetic stability following DNA base damage. (thermofisher.com)

Anatomy4

Organisms45

Chemicals and Drugs56

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes89

Disciplines and Occupations6

Technology, Industry, Agriculture2

Information Science31

Health Care11

Geographicals2

Genome14

Alignments6

Bioinformatics4

Genes and proteins1

Membrane protein7

Homology6

Shape similarity3

Similar sequences5

Residues8

Encodes4

Blastp3

CDNA sequences1

Genomic Sequence2

FASTA1

Prediction8

Structures11

Soluble proteins1

Algorithm4

Functional similarities2

Arabidopsis4

Homologous4

GenBank2

Binding Sites13

Structural2

Annotation1

Residue3

Mass Spectrometry Data1

Pairwise3

Genomes1

Recombinant3

Differences3

Function17

Receptors4

Clusters1

Myelin Basic P1

Interaction1

Biochemical1

Molecular6

Consists1

Signal transduction1

Methods5

Chromosome3

Antigens2

Biological1

Clustering1

Peptide4

Motif1

Divergence2

Specificity1

Transmembrane2

Human8

Regulate3

Structure8

Antibodies1

Multiple protein1

Analysis4

Identical2

Pathogen1

Datasets2

Variants1

Mechanism2

Yeast3

BLAST9

Nucleotide-nucleotide1

Genetic1