Pairs of residues predict contacting residue pairs protein residues. Medical search. Frequent questions

Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
The residue contact information can be incorporated in structure prediction in several different ways: It can be incorporated as statistical potentials or it can be also used as constraints in ab initio structure prediction. (biomedcentral.com)
To seek the most effective definition of residue contacts for template-based protein structure prediction, we evaluated 45 different contact definitions, varying bases of contacts and distance cutoffs, in terms of their ability to identify proteins of the same fold. (biomedcentral.com)
A proper encoding of residue contact information is crucial for structure prediction because in principle, a full distance map or a residue contact map has sufficient information for reconstructing the tertiary structure of a protein[ 25 ]. (biomedcentral.com)
This document outlines metrics used in contact prediction in the past and provides feedback from the CASP13 contact prediction assessor, Andras Fiser. (predictioncenter.org)
Assessment is concentrated on the long-range contacts (separation of the interacting residues of at least 24 positions along the sequence) as these are the most valuable for structure prediction. (predictioncenter.org)
David Baker/Rosetta and Jinbo Xu/RaptorX-Contact groups speculate that we need 1.5L ~ 2L contacts to obtain good contact-assisted ab initio contact prediction. (predictioncenter.org)
Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. (biomedcentral.com)
Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. (biomedcentral.com)
We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. (biomedcentral.com)
These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins. (biomedcentral.com)
Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (biomedcentral.com)
Inspired by the success of non-linear models in TBM methods, we would like to study if we can improve TBM methods' model accuracy using more advanced neural network architecture such as deep residual network which has proven very successful in protein residue-residue contacts prediction. (biomedcentral.com)
So for the structure prediction based on the sequence, we first downloaded a multiple sequence alignment of Ras (PF00071) from the Pfam database and generated one for our protein PAH with PSI-BLAST and ClustalW. (tu-muenchen.de)
However, for structure prediction more distant residues are more interesting as connections between distant amino acids might lead to its compact structure. (tu-muenchen.de)
Contact map of the best 104 residue pairs of the freecontact prediction (red). (tu-muenchen.de)
We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. (edu.sa)
The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. (edu.sa)
The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9. (edu.sa)
White squares represent protein pairs where no prediction was made, usually because the proteins exceed ~4000 amino acids. (predictomes.org)
Protein pairs for which there is at least one structure in the PDB are marked by an orange dot in the matrix (even if the structure does not match the prediction). (predictomes.org)
Therefore, the prediction of MCP structures will be performed for surface analysis to facilitate the verification of the predicted LEs. (biomedcentral.com)
You can upload your own contact restraints to be used for the structure prediction. (tu-berlin.de)
Whilst elicitation of the symptoms of allergic contact computational sensitization hazard prediction dermatitis (ACD) upon subsequent exposure to rulebase tools such as Deduction and Estimation the same or cross-reactive chemicals. (cdc.gov)

ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residue-residue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix. (biomedcentral.com)
TBM method predicts the structure of query protein by modifying the structural framework of its homologous protein with known structure in accordance with template-query alignment. (biomedcentral.com)
Subsequentely, we calculated the structural models for both proteins. (tu-muenchen.de)
Because only a few sugar porter structures have been determined, mechanistic models have been constructed by piecing together structural states of distantly related proteins. (bvsalud.org)
Functional and structural characterization of human adrenoleukodystrophy protein (ALDP). (elifesciences.org)
Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. (lookformedical.com)
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. (leibniz-fli.de)
His calculations on protein circular dichroism spectroscopy, a key technique in structural biology, are the most accurate to be published. (nottingham.ac.uk)
Advancements in areas such as ionization have helped to create growing applications of MS in the clinic, including: Cross-linking MS (XL-MS) is an important a tool in structural biology, revealing information on protein interaction networks within biological samples, from proteins to macromolecular complexes, cells and even tissues. (technologynetworks.com)
Among others, it provides insights for: Omics Clinical diagnostics Structural biology Amino acid Polypeptide chains α-Helixes Complex of protein molecule PRIMARY STRUCTURE TERTIARY STRUCTURE SECONDARY STRUCTURE QUATERNARY STRUCTURE PRIMARY STRUCTURE MS is a key tool for the detection of many environmental contaminants, both well known and emerging. (technologynetworks.com)
The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)
Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins. (embl.de)
The amino acid residues important in these kringle/ligand binding interactions have been proposed by structural determinations, and their relative importance quantified by site-directed mutagenesis experimentation. (embl.de)

These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range reconstruction). (wikipedia.org)
Motivated by the development of techniques for determining the primary (amino acid) sequence of proteins by Frederick Sanger in 1955, Zuckerkandl and Pauling postulated that such sequences could be used to infer not only the phylogeny relating the observed protein sequences, but also the ancestral protein sequence at the earliest point (root) of this tree. (wikipedia.org)
All three tables show the position of the first residue in column one with its corresponding amino acid (column 2) and of the second residue in column three with its amino acid in column four. (tu-muenchen.de)
To find the PAE value of a specific amino acid pair, hover over the PAE plots. (predictomes.org)
The DAQ score assesses the consistency of amino acid assignment in protein structure models with local density from cryo-EM maps. (springernature.com)
Therefore, we present our new approach, Deep-learning-based Amino acid-wise model Quality (DAQ) score, for cryo-EM protein model validation. (springernature.com)
Deep-learning-based Amino acid-wise model Quality (DAQ) score computes the likelihood that the local density corresponds to different amino acids, atoms, and secondary structures, estimated via deep-learning, and assesses how well the amino acid assignment in the atomic protein structure model is consistent with that likelihood. (springernature.com)
Therefore, we trained a deep convolutional neural network that can predict protein secondary structure, amino acid type and atom types at the same time via multi-task training. (springernature.com)
DAQ score can indicate if an amino acid residue assigned to a local density is likely to be incorrect, even in cases where the protein sequence is misaligned along an otherwise correct main-chain trace. (springernature.com)
Our results suggest that incorrect amino acid assignment can happen even when the residue has reasonably high local density cross-correlation and appropriate stereochemical geometry. (springernature.com)
The resulting HPlm contains a heavy chain of 561 amino acid residues, originating from the N-terminus of HPlg, doubly disulfide-linked to a light chain of 230 amino acid residues. (embl.de)
The heavy chain of HPlm consists of five repeating triple-disulfide-linked peptide regions, c. 80 amino acid residues in length, termed kringles (K), that are responsible for interactions of HPlg and HPlm with substrates, inhibitors and regulators of HPlg activation. (embl.de)

This table lists all predicted inter-residue contacts between the two proteins. (predictomes.org)

The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. (edu.sa)

Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
The evolutionary variation in sequences is limited by a number of necessities, like e.g. the maintenance of favourable interactions in direct residue-residue associations. (tu-muenchen.de)
The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.com)
Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
The p.Asn173His mutation affects a residue in the forkhead domain that is 100% conserved among vertebrate orthologs and is predicted to participate in protein-protein interactions. (molvis.org)
rium properties, completely determined by the interactions within crystal structures of 38 nonhomologous proteins, we find that it the system. (lu.se)
Sequestration of malaria parasite in the human placenta is mediated by interactions between chondroitin sulphate A (CSA) on the syncytiotrophoblasts and proteins expressed on the surface of infected human erythrocytes. (biomedcentral.com)
Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. (asm.org)

A larger distance cutoff is often advantageous for capturing spatial arrangement of the secondary structures which are not physically in contact. (biomedcentral.com)
Although protein structures have been solved by experiments at an increasing rate, a flood of new sequences have been determined even more rapidly due to the advance of sequencing technologies[ 6 , 7 ]. (biomedcentral.com)
Analysis of non-redundant SCOP structures from Y. Zhang's group shows that the average number of short, medium, and long-range contacts of a well folded protein domain is 0.3*L, 0.4*L, and 1.2*L, respectively. (predictioncenter.org)
Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. (biomedcentral.com)
According to the huge number of known sequences and the low quantity of known structures it is an important challenge to predict the structure of proteins from sequence information alone. (tu-muenchen.de)
Here, we have combined coevolution analysis and comparative modeling, to predict structures of the entire sugar porter superfamily in each state of the transport cycle. (bvsalud.org)
To compare predicted and experimentally-determined PDB structures, click on "superimpose PDB. (predictomes.org)
Therefore, before undertaking mutagenesis studies, we recommend downloading structures of interest, relaxing them using (AMBER) , and then identifying interacting residues using PISA . (predictomes.org)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. (lookformedical.com)
Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
In general, immunobiologists have developed an integrated method for vaccine development based on analyzing protein sequences and structures of target viruses [ 10 ]. (biomedcentral.com)
However, only few protein structures have been currently resolved for the Iridoviridae family, none of which are associated with the outer capsid proteins. (biomedcentral.com)
We further tested DAQ on 399 pairs of PDB entries of protein structures of high sequence identity built from cryo-EM maps in which the models differ by more than 1 Å RMSD from each other. (springernature.com)

Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation CHEMISTRY-A EUROPEAN JOURNAL. (nottingham.ac.uk)
Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)

Mostly the sequence of the interested protein is part of an evolutionarily related family of sequences, which are probable to have the same fold fundamentally. (tu-muenchen.de)
We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. (edu.sa)
They act to fasten the protein to an AT RICH SEQUENCE in the DNA. (lookformedical.com)
You can enter a single-chain protein sequence in FASTA format with or without the FASTA header line. (tu-berlin.de)
After predicting the contacts for the given target sequence our server runs template retrieval. (tu-berlin.de)
But you may deactivate "Domain splitting" to predict the whole input sequence at once by deselecting the check box when using the 'automatic' modeling method. (tu-berlin.de)

We found that overall the residue contact pattern can distinguish protein folds best when contacts are defined for residue pairs whose Cβ atoms are at 7.0 Å or closer to each other. (biomedcentral.com)
For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to opposite directions. (biomedcentral.com)
3. Definition of contacts (residue centers and distance thresholds) (i) The definition historically used in CASP: a pair of residues is defined to be in contact when the distance between their Cβ atoms (Cα in case of glycine) is smaller than 8.0 Å. (predictioncenter.org)
A pair of residues is defined to be in contact when the distance between their C-beta atoms (C-alpha in case of glycine) is less then 8 Ångstrøm. (tu-berlin.de)
containing all atoms within 8 of each His residue. (lu.se)
If the residue is exposed to water it is probably HIP (especially if there is a strong H-bond to one of the atoms), otherewise it is probably neutral, unless it interacts with Asp, Glu, or another negatively charged residue. (lu.se)

The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. (biomedcentral.com)
Plasminogen, HGF/SF and HGF1/MSP represent paradigmatic examples of the modern, multi-domain proteins typically associated with vertebrate organisms and illustrate a novel evolutionary pathway that led to the emergence of molecules with growth regulatory activity from proteolytic enzymes. (embl.de)

It is of fundamental importance in determining PROTEIN CONFORMATION. (lookformedical.com)
If alternative conformations are present, remove the residue conformation (found in point 4 above) with the lowest occupancy and note which residues are disordered. (lu.se)

Then a subset of the predicted residue contact pairs is used to fold up any protein of the family into an approximated 3D structure. (tu-muenchen.de)
To display a subset of proteins in the matrix, use "row" and "column" menus. (predictomes.org)

Also, previous assessments evaluated predictions on medium + long-range contacts (12+ residues separation). (predictioncenter.org)
If you like to obtain predictions for longer proteins, please contact us. (tu-berlin.de)

Today, computational methods for ancestral reconstruction continue to be extended and applied in a diversity of settings, so that ancestral states are being inferred not only for biological characteristics and the molecular sequences, but also for the structure or catalytic properties of ancient versus modern proteins, the geographic location of populations and species (phylogeography) and the higher-order structure of genomes. (wikipedia.org)
This information is useful for the analyzing genetic relatedness of proteins and species. (lookformedical.com)
The basis of hapten- molecular mechanisms of the sensitization pro- protein binding work is the hypothesis that upon cess will result in novel opportunities for the skin absorption, only protein-reactive chemicals development of alternative methods for assessing (or those that can be metabolically or chemically skin sensitization hazard and relative potency of converted to protein-reactive species) are able to chemicals. (cdc.gov)

The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. (lookformedical.com)

These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. (asm.org)
1987. Statistical correlations for predicting the partition coefficient for nonpolar organic contaminants between aquifer organic carbon and water. (cdc.gov)

Each contact is assigned a probability p [0;1] reflecting confidence of the assignment. (predictioncenter.org)
the real number p indicates probability / confidence of the two residues being in contact, and is the range 0.0 - 1.0. (tu-berlin.de)
Contacts are listed according to the decreasing probability p. (tu-berlin.de)

His research spans a wide range, from the quantum chemistry of small molecules and the spectroscopic properties of proteins, to the application of state-of-the-art statistical and computer science methodology to problems in bioinformatics, drug design and sustainable chemistry. (nottingham.ac.uk)
are usually modeled with several residues in alternative conforma- basis of elementary statistical mechanics and generic features of tions, each with its own set of AMSDs. (lu.se)

The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
Or we simply can use the number of long-range contacts in the native structure? (predictioncenter.org)
Protein structure is fundamentally important to understand protein functions. (biomedcentral.com)
To find out which residue pairs are lying in the 3D structure close to each other, one uses pair correlations in the multiple alignments. (tu-muenchen.de)
This is subsequently refined with different techniques to generate a finished structure for the protein of interest. (tu-muenchen.de)
In grey the contact map of the pdb structure 121p is shown. (tu-muenchen.de)
Based on the structure, we performed integrative analysis of the cellular trafficking, protein thermostability, ATP hydrolysis, and the transport activity of representative mutations. (elifesciences.org)
Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)
This is referred to as the primary structure of proteins. (lookformedical.com)
Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure. (lookformedical.com)
The primary data, structure factors of Bragg reflections, AMSDs can be predicted solely on the basis of packing density. (lu.se)
Yet, the local yield a set of mean atomic positions r 0 density, averaged over volume elements of 0.1-1 nm3, varies k r k that define the ``ground-state'' protein structure, or, if resolution permits, a small substantially within a protein (14, 17, 18). (lu.se)
A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)
Thus, it's natural for us to apply deep learning for structure quality assessment of protein models from cryo-EM maps. (springernature.com)
Then the local predicted features by deep learning are compared with amino acids in the structure built from the EM map to computer DAQ scores. (springernature.com)
3. Are there any missing parts of the structure (check remark 465, missing residues, but also the start and the end of the file). (lu.se)

Specific protein-binding measures are often used as assays in diagnostic assessments. (lookformedical.com)
These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. (biomedcentral.com)
Thus, the principle of protein or peptide haptenation could be used in in vitro assays to predict the sensitization potential of a new chemical entity. (cdc.gov)

The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)

This gene encodes a large protein with an estimated molecular weight of 350 kDa, and can be divided into six Duffy-binding-like domains (DBL 1-6) based on several conserved cysteines. (biomedcentral.com)

Engineered mutations to the 10E8 paratope at light-chain solvent-exposed residues that add positive charge or hydrophobic sidechains proved to increase antibody association to anionic phospholipid vesicles in vitro and also boosted neutralization potency 27 . (elifesciences.org)

When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. (biomedcentral.com)
The model accuracy of TBM method critically depends on protein features and the scoring functions that integrate these features. (biomedcentral.com)

On aver- comprising some 1015 protein molecules. (lu.se)

One of the key molecular events in skin sensitization is protein haptenation, i.e. the chemical modification of self-skin protein(s) thus forming macromolecular immunogens. (cdc.gov)

Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. (biomedcentral.com)

Antibodies can target epitopes on integral membrane proteins very near to the lipid bilayer surface, even those partially embedded within the headgroup region. (elifesciences.org)

An in-house analysis shows that the three definitions on CASP targets agree in 80+ % of cases (i.e., contact between two residues according to measure x is also a contact according to measure y). (predictioncenter.org)
More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
Likewise, the ProQ/FinO domain-containing protein RocC of Legionella pneumophila interacts with only one trans -acting sRNA (RocR) to repress post-transcriptionally multiple mRNA targets 6 . (nature.com)
Protein-protein interaction inhibition (2P2I): fewer and fewer undruggable targets. (leibniz-fli.de)

NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)
in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)

To detect unstructured segments of proteins that are predicted to become ordered when folded with another protein, look for large increases in pLDDT score between the models and baseline (the pLDDT value for the protein in the presence of a non-interacting partner). (predictomes.org)

In the case of threading, alignment accuracy strongly influences the fraction of common contacts identified among proteins of the same fold, which eventually affects the fold recognition accuracy. (biomedcentral.com)
The largest deterioration of the fold recognition was observed for β-class proteins when the threading methods were used because the average alignment accuracy was worst for this fold class. (biomedcentral.com)
Residue contacts defined by Cβ−Cβ distance of 7.0 Å work best overall among tested to identify proteins of the same fold. (biomedcentral.com)
We also found that effective contact definitions differ from fold to fold, suggesting that using different residue contact definition specific for each template will lead to improvement of the performance of threading. (biomedcentral.com)
In particular, in terms of alignment accuracy measured with TM-score, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 56, 13, and 11%, respectively, on template-query pairs at the similarity of fold level from SCOPe data. (biomedcentral.com)

Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. (leibniz-fli.de)

DNA-binding motifs, first described in one of the HMGA PROTEINS: HMG-I(Y) PROTEIN. (lookformedical.com)

PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks. (leibniz-fli.de)
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. (leibniz-fli.de)

Contacts in target proteins. (predictioncenter.org)
sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
Subsequent un-anchoring of FGFR-bound-FGF from the source cell membrane dissociates cytoneme contacts and delivers FGF target-specifically to ASP cytonemes for paracrine functions. (biorxiv.org)
The prevalence and similarities of these signaling filopodia suggest that the polarized target-specific morphogen exchange through filopodial contacts is an evolutionarily conserved signaling mechanism. (biorxiv.org)
We asked: (1) How do cytonemes recognize a specific target cell and form signaling contacts? (biorxiv.org)

Characterisation of a cluster of genes encoding Theileria annulata AT hook DNA-binding proteins and evidence for localisation to the host cell nucleus. (lookformedical.com)

proteins could carry out their biological functions. (lu.se)

We developed a novel method for quality assessment, which can evaluate protein models from cryo-EM maps via pre-trained deep convolutional neural networks. (springernature.com)
Contact allergens are present in the natural mate potency and are not used as risk assessment environment, but the potential exposure to aller- tools in safety support (8). (cdc.gov)

To view the evolutionary rate of change of individual residues (low change, high conservation), click and drag over the region of interest. (predictomes.org)
Further analysis of the proposed sulphate and predicted CSA-binding site indicates either none or very low level of conservation among the critical interacting residues. (biomedcentral.com)

In this review, we consider some of the theoretical aspects of protein haptenation, how mechanisms of protein haptenation can be investigated experimentally and how we can use such knowledge in the development of novel, alternative approaches for predicting skin sensitization potential in the future. (cdc.gov)

Constructing glucagon like peptide-1 receptor fused with derivatives of GFP for visualizing protein-protein interaction in living cells. (leibniz-fli.de)

In contrast, traditional models predict that the signal presentation from the source via free secretion and extracellular diffusion is a non-selective process. (biorxiv.org)

I am in need of some help regarding the ab initio folding of a protein in the presence of its cofactor. (rosettacommons.org)
I would like to make an ab-initio-relax in the presence of the cofactor and constraints build from what I know about the cofactor-protein interaction. (rosettacommons.org)

For our protein two domains are included (ACT and Biopterin domain). (tu-muenchen.de)
Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
If RBO Aleph detects multiple domains, it is much easier to predict each domain separately. (tu-berlin.de)
Taxonomic distribution of proteins containing KR domain. (embl.de)
The complete taxonomic breakdown of all proteins with KR domain is also avaliable . (embl.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing KR domain in the selected taxonomic class. (embl.de)

In RL evaluation, the previous assessments mainly discussed results on the L/5 long-range contact lists. (predictioncenter.org)

Intriguingly, a crucial loop from A4 DBL 3X which provides the important Gly and Lys residues that chelate the bound sulphate is missing or significantly altered in all other DBL domains that interact with CSA. (biomedcentral.com)

is a program that takes a multiple alignment and can calculate the mutual information score and the corrected norm contact score. (tu-muenchen.de)

In addition, you can precisely expand it by adding individual residues - or with a single click to find empty pockets in your protein. (biosolveit.de)

However, accurate template-query alignment and template selection are still very challenging, especially for the proteins with only distant homologs available. (biomedcentral.com)

Small molecule protein-protein interaction inhibitors as CNS therapeutic agents: current progress and future hurdles. (leibniz-fli.de)

The var2CSA gene, which is a member of the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family, may have an important role in PAM disease and immunity. (biomedcentral.com)
Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)

The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) encoded by the var2CSA gene is believed to be the main parasite ligand for CSA-mediated placental binding. (biomedcentral.com)

Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. (elifesciences.org)

Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
FGF-source and recipient ASP cells extend cytonemes that present FGF and FGFR on their surfaces and reciprocally recognize each other over distance by contacting through CAM-like FGF-FGFR binding. (biorxiv.org)

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