Protein complexes predict contacting residue pairs protein residues. Medical search. Frequent questions

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)

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)
Structural comparison of protein-protein interfaces provides valuable insights into the functional relationship between proteins, which may not solely arise from shared evolutionary origin. (biomedcentral.com)
A few methods that exist for such comparative studies have focused on structural models determined at atomic resolution, and may miss out interesting patterns present in large macromolecular complexes that are typically solved by low-resolution techniques. (biomedcentral.com)
Protein-protein interactions play important functional roles in almost all biological activities, including, but not restricted to, signal transduction, gene regulation, catalytic enzymatic activities and structural roles [ 1 ]. (biomedcentral.com)
The currently available implementation for this method initially defines interfacial residues using atomic details, and then uses positions of the Cα atoms for structural alignment and scoring, and includes a sequence-order dependent version [ 10 ] and a sequence-order independent version [ 11 ]. (biomedcentral.com)
His calculations on protein circular dichroism spectroscopy, a key technique in structural biology, are the most accurate to be published. (nottingham.ac.uk)
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)
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)
In other words, amino acids are the structural elements of all proteins . (ainews.one)
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. (lookformedical.com)
We showed that Gαq coupling to AT1R involved a large number of residues spread across the receptor, whereas fewer structural regions of the receptor contributed to ß-arrestin coupling regulation. (bvsalud.org)
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)
Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (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)
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. (leibniz-fli.de)
1991), none of the the structural details of the heterogeneous protein surface and experimental studies mentioned so far could provide un- takes into account a variety of short-range interactions, direct ambiguous information about oligomer structure. (lu.se)

At the center of protein-protein interactions are the binding surfaces, or interfacial residues which form contacts between binding partners and stabilize protein complexes. (biomedcentral.com)
Superposition is based on best match of interfacial residues. (predictomes.org)

To view the evolutionary rate of change of individual residues (low change, high conservation), click and drag over the region of interest. (predictomes.org)
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)

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)

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)

All-atom simulations of 4E10, PGZL1, 10E8 and LN01 docked onto HIV-like membranes consistently form phospholipid complexes at key complementarity-determining region loop sites, solidifying that stable and specific lipid interactions anchor bnAbs to membrane surfaces. (elifesciences.org)
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)
Characterization and classification of protein-protein interactions would allow us to organize information in protein-protein interaction networks, to make predictions on their function, as well as to facilitate drug design targeted at interfering with those disease-associated protein-protein interactions. (biomedcentral.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)
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)
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)
Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior of interface interactions and their effect on the coupling of proteins. (bvsalud.org)
Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. (bvsalud.org)
Although they are critically important in protein-protein interfaces it is challenging to determine which amino acid pair interactions are cooperative. (bvsalud.org)
This observation indicates that cooperativity of GPCR:G protein interactions is necessary for the coupling and selectivity of G proteins and is thus critical for receptor function. (bvsalud.org)
We have identified subnetworks containing polar and hydrophobic interactions that are common among multiple GPCRs coupling to different G protein subtypes (Gs, Gi and Gq). (bvsalud.org)
As the assembly was carried out in the absence of ATP, this suggests that formation of the holoenzyme from the individual subcomplexes is solely driven by protein-protein interactions at the interface. (upstate.edu)
Unlike reversible disassembly, which requires ATP hydrolysis on V 1 to break protein-protein interactions, Oxr1p mediated disassembly of V-ATPase is ATP independent and therefore a novel mode of activity regulation. (upstate.edu)
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)

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)

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

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)
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)
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)
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)
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)
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)

Molecular analysis suggested that Esc2p contributed to silencing in a manner similar to Sir1p and probably helped recruit or stabilize the other Sir proteins, while Htz1p present at HMR assembled a specialized chromatin structure necessary for silencing (Dhillon, 2000). (sdbonline.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)

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)
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)
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)
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)
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)
We applied our model to two protein structures as examples, and verified the validity of our model using various types of experimental data. (biomedcentral.com)
Historically, allosteric regulation has typically been defined in quaternary structures (e.g., hemoglobin), but now it is recognized as an intrinsic property of all proteins, including monomeric structures [ 8 ]. (biomedcentral.com)

The latter is useful for revealing potential biological relationships between different complexes, and a suitable method to directly compare protein-protein interfaces across randomly selected protein complexes and to quantitatively assess their pairwise similarities is highly desirable. (biomedcentral.com)
Depending on the specific biological question being asked, methods for protein-protein interface comparison with different focuses have been developed. (biomedcentral.com)
Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. (mdpi.com)
The cyber twins can be used to simulate complex biological processes and deduce effects of medical treatments. (hep.com.cn)

Computational modeling of the STAT3D PROTAC ternary complex predicted two surface lysines on STAT3, K601 and K626 as potential ubiquitination sites for the PROTAC bound E3 ligase. (bvsalud.org)

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)

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)

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)
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)

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)

The modeling platform developed here uncovers insights into lipid participation in antibodies' recognition of membrane proteins and highlights antibody features to prioritize in vaccine design. (elifesciences.org)
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)
Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)
These residues can not only be targeted by broad spectrum antibodies and drugs, mutations in them can generate new strains of coronavirus resulting in future epidemic. (biorxiv.org)
Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)
18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)

We developed a coarse-grained method, PCalign, to quantitatively evaluate physicochemical similarities between a given pair of protein-protein interfaces. (biomedcentral.com)
This method uses an order-independent algorithm, geometric hashing, to superimpose the backbone atoms of a given pair of interfaces, and provides a normalized scoring function, PC-score, to account for the extent of overlap in terms of both geometric and chemical characteristics. (biomedcentral.com)
PCalign is a useful method in recognizing shared chemical and spatial patterns among protein-protein interfaces. (biomedcentral.com)
While these approaches provide insights into the mechanism of protein-protein recognition, they are not suitable for measuring similarities between a given pair of protein-protein interfaces. (biomedcentral.com)
Gao and Skolnick developed the dynamic programming-based algorithm Ialign [ 10 ] to detect protein-protein interfaces with shared geometric patterns. (biomedcentral.com)
developed I2I-SiteEngine [ 12 ] to compare the physicochemical properties of the functional groups forming protein-protein interfaces, which uses an algorithm similar to pharmacophore mapping. (biomedcentral.com)
We also found that the hot spots in protein binding interfaces have significantly high EVT values, which suggests that they play roles in mediating signal communication between protein domains. (biomedcentral.com)
Predicting protein-protein interfaces as clusters of optimal docking area points. (leibniz-fli.de)

Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. (elifesciences.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)
Infection of human cells by the novel coronavirus (SARS-Cov-2) involves the attachment of the receptor binding domain (RBD) of the spike protein to the peripheral membrane ACE2 receptors. (biorxiv.org)
For example, alkaline vacuole/lysosome are deficient in autophagy, Golgi pH regulates its ability to glycosylate proteins and failure to maintain endosomal pH perturbs with its ability to recycle receptors to the Plasma membrane or, the trans-Golgi. (upstate.edu)
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)
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)
Deciphering soluble and membrane protein function using yeast systems. (leibniz-fli.de)
The hOAT3 protein was shown to be localized in the basolateral membrane of renal proximal tubules and the hOAT3 gene was determined to be located on the human chromosome 11q12-q13.3 by fluorescent in situ hybridization analysis. (aspetjournals.org)

Therefore, it is important to determine how the induced signal is transmitted via an amino acid network and how the allosteric effects are represented in a protein structure. (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)

Each hormone peptide has its own class B type G-protein coupled receptor 19 , 21 functioning along identical receptor activating schemes (Fig. 1c ). (nature.com)
Significant research effort for drug design against COVID-19 is focused on the receptor binding domain of the spike protein, although this region is prone to mutations causing resistance against therapeutics. (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)
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)
In this work we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with G proteins. (bvsalud.org)
Constructing glucagon like peptide-1 receptor fused with derivatives of GFP for visualizing protein-protein interaction in living cells. (leibniz-fli.de)

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)
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)
The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)

6 Significantly, the sites in S protein have been demonstrated to be vulnerable to acquire mutations. (biorxiv.org)

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)

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

Each contact is assigned a probability p [0;1] reflecting confidence of the assignment. (predictioncenter.org)

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)
This information is useful for the analyzing genetic relatedness of proteins and species. (lookformedical.com)

Mutation on these residues can lead to new strains of coronavirus with different degrees of infectivity and virulence. (biorxiv.org)
The most ubiquitous D614G mutation is predicted ab-initio from our model. (biorxiv.org)

Also, previous assessments evaluated predictions on medium + long-range contacts (12+ residues separation). (predictioncenter.org)
AlphaFold's Protein Structure Database provides open access to protein structure predictions for the human proteome and 20 other organisms to accelerate scientific research. (ainews.one)

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)
The RNA chain is decoded and translated by ribosomes to produce a polypeptide sequence, otherwise known as a protein. (ainews.one)
For example, the sequence AUG (in the mRNA) is a codon that specifies the amino acid methionine, which almost always specifies the beginning of a protein. (ainews.one)
They act to fasten the protein to an AT RICH SEQUENCE in the DNA. (lookformedical.com)

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

Normalized binding propensity of amino acid residues in different organisms. (biomedcentral.com)
NASCENT: An automatic protein interaction network generation tool for non-model organisms. (leibniz-fli.de)

The histone H2A.F/Z (H2AZ) variant is a functionally distinct, highly conserved histone subgroup that likely represents a separate evolutionary lineage of histone H2A proteins. (sdbonline.org)

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)
While individual V 1 and V o subcomplexes are locked in specific rotary states, the in vitro assembled complexes populated three rotary states, similar to what was previously observed for native V-ATPase. (upstate.edu)

This pairing allows cells to copy information from one generation to another and even fix errors in the information stored in the sequences. (ainews.one)
By now you get the idea that cells generate proteins, which are sequences of amino acids. (ainews.one)

Network properties of complex human disease genes identified through genome-wide association studies. (leibniz-fli.de)

Insights from the work on formamide and other small amides have been applied to studies of proteins and have led to significant improvements in the calculation of the circular dichroism of proteins from first principles. (nottingham.ac.uk)
This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components. (bvsalud.org)

G protein-coupled receptors engage both G proteins and ß-arrestins, and their coupling can be biased by ligands and mutations. (bvsalud.org)
Allosteric communication in proteins can be induced by the binding of effective ligands, mutations or covalent modifications that regulate a site distant from the perturbed region. (biomedcentral.com)

Specific protein-binding measures are often used as assays in diagnostic assessments. (lookformedical.com)

We hypothesized that the residues with high EVT values play important roles in allosteric signalling, and found experimental evidences supporting the idea. (biomedcentral.com)
Experimental binding data (ΔΔG values) of alanine-mutated interface residues of known protein complexes have been mostly widespread for estimating the residue-contribution to the binding event (i.e. finding the binding hot spots). (biomedcentral.com)

Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction. (leibniz-fli.de)

To find the PAE value of a specific amino acid pair, hover over the PAE plots. (predictomes.org)

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)

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)

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)
A protein called p63, which is closely related to another protein that suppresses the formation of tumors, plays an essential role in detecting and responding to DNA damage. (elifesciences.org)

A skin sensitizer is a chemical with an intrinsic currently reliant on in vivo methods such as the ability to induce contact allergy. (cdc.gov)
Contact Dermatitis 2005: 53: 189-200 absence of in vivo animal data. (cdc.gov)
Nucleosomes impose a block to transcription that can be overcome in vivo by remodeling complexes such as SNF/SWI and histone modification complexes such as SAGA. (sdbonline.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)

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)
In the clinic, MS is becoming a vital tool, able to detect and quantitate trace levels of known and unknown targets in complex samples. (technologynetworks.com)
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)
Protein-protein interaction inhibition (2P2I): fewer and fewer undruggable targets. (leibniz-fli.de)

Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. (elifesciences.org)
Specific distribution of PI lipids is regulated, either by the localization of a kinase-phosphatase pair or, by vesicular and non-vesicular lipid transport. (upstate.edu)

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)

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)
The DAQ score assesses the consistency of amino acid assignment in protein structure models with local density from cryo-EM maps. (springernature.com)
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)
Or we simply can use the number of long-range contacts in the native structure? (predictioncenter.org)
This is referred to as the primary structure of proteins. (lookformedical.com)
Protein structure is fundamentally important to understand protein functions. (biomedcentral.com)
To understand allosteric regulation, it is important to identify the remote sites that are affected by the perturbation-induced signals and how these allosteric perturbations are transmitted within the protein structure. (biomedcentral.com)
In this study, by constructing a protein structure network and modeling signal transmission with a Markov random walk, we developed a method to estimate the signal propagation and the resulting effects. (biomedcentral.com)
The presented method used a protein structure network constructed based on the intrinsic assumption that network centrality measures (i.e. relative importance of a node within the network) represent various methods of signaling transmission [ 27 ]. (biomedcentral.com)

Our results reveal a strong co-dependency in the formation of interface GPCR:G protein contacts. (bvsalud.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)

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

Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)
We hypothesized that the residues with high EVT values play important roles in allosteric signaling. (biomedcentral.com)

Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
Oxr1p belongs to the group of TLDc domain containing proteins that are highly conserved in higher eukaryotes. (upstate.edu)

These common subnetworks along with G protein-specific subnetworks together confer selectivity to the G protein coupling. (bvsalud.org)

The model accuracy of TBM method critically depends on protein features and the scoring functions that integrate these features. (biomedcentral.com)

Anatomy11

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Analytical, Diagnostic and Therapeutic Techniques and Equipment45

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Prediction12

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