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  • motifs
  • PPR proteins are involved in RNA processing, and mapping the selection data to a predicted consensus structure of an array of PPR motifs suggests that these residues are likely to form base-specific contacts to the RNA ligand. (pnas.org)
  • JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. (biomedcentral.com)
  • We therefore present a comparative docking protocol in HADDOCK using critical motifs, and use it to "predict" the various selectivity profiles of several major αKTX scorpion toxin families versus K v 1.1, K v 1.2 and K v 1.3. (mdpi.com)
  • Repositioning the guide sequence of U25 upstream of box D instead of D′ revealed that both C/D motifs have the potential to function as guide centers, but, surprisingly, there was no alteration in protein cross‐linking. (embopress.org)
  • Engineering zinc finger protein motifs for specific binding to double-stranded DNA is critical for targeted genome editing. (biomedcentral.com)
  • homologous
  • Specific examples of this work include the automatic modeling of antibody variable domains, the general modeling of homologous proteins and studies of DNA base-pair mismatches. (stanford.edu)
  • During the development of selective peptides against highly homologous targets, a reliable tool is sought that can predict information on both mechanisms of binding and relative affinities. (mdpi.com)
  • And similarly, will homologous sites in related but distinct viral strains evolve at similar rates, or do the nature of the viral strain and the infected host organism impose stronger influences on site-specific evolutionary rates than the location of a site in the protein structure? (royalsocietypublishing.org)
  • significantly
  • We show that it correctly predicts some contacts and that predicted residues tend to be significantly closer to each other than other pairs of residues in the same domains. (biomedcentral.com)
  • We measured the co-evolution between any two modified sites in a particular protein using the mutual information ( MI ) algorithm (see explanation in the figure below) and extracted those pairs that are significantly co-evolving in comparison to pairs of non-modified residues in the same protein(s) with the same type of amino acid and placed on similar protein regions (ordered or disordered). (embl.de)
  • This catalytic role is verified by experiments (including replacement by norleucine and selenomethionine), which show that mutation of this residue significantly affects k cat , without changing K M for phosphite. (rsc.org)
  • topology
  • Over a set of test proteins, both gave good results, with the topology method performing slightly better. (biomedcentral.com)
  • Although contact maps based on the static structure of the complex give an initial approximation to the physical communication network, the inclusion of dynamical correlations provides a more accurate picture of the network topology and approximates the strength of the allosteric signal that can be related to experimental observations. (pnas.org)
  • For a given fold topology, contact maps generate unweighted networks representing the residue connectivity ( 9 ). (pnas.org)
  • Conservation
  • Sensitive conservation analyses have been proposed to detect functional sites within proteins ( 18 ⇓ - 20 ) and have further been used for the identification of protein-binding sites ( 21 ⇓ ⇓ ⇓ ⇓ - 26 ). (pnas.org)
  • However, conservation does not provide mutual information between interacting partners so as to identify the residue pairs in contact. (pnas.org)
  • Understanding sequence conservation is obviously important for the understanding of protein evolution and ultimately for understanding phenomics. (labo.de)
  • It also uses the machine learning method, which integrates Position-Specific Scoring Matrix (PSSM), sequence distance, residue covariance, residue conservation, relative residue distance of two helices and helix number to predict helix-helix contacts. (omictools.com)
  • The pathways of signal transduction favored by the network of interresidue contacts and the role conservation plays in these pathways remain to be established. (pnas.org)
  • Database of pre-evaluated conservation and specialization scores for multi-member families of human proteins. (ucsf.edu)
  • algorithm
  • According to our own evaluations performed at a resolution of +/− two residues, the predictors we trained with the random forest algorithm were our top performing methods with average top 10 prediction accuracy scores of 85.13% (short range), 74.49% (medium range), and 54.49% (long range). (springer.com)
  • The search is performed with a simulated annealing algorithm directly in contact space. (biomedcentral.com)
  • The superior performance over existing RNA-binding residue prediction methods indicates the importance of the gradient tree boosting algorithm combined with the optimal selected features. (biomedcentral.com)
  • The algorithm decomposes proteins into set of overlaping segments of 9-13 residues, then tries to match them using root mean square distance metric. (edu.pl)
  • biological
  • The modular assembly of proteins is a key determinant in the regulation of biological systems. (pnas.org)
  • Determining these protein-RNA binding residues can help to elucidate the underlying mechanisms, to control biological processes, or to design RNA-based drug. (biomedcentral.com)
  • predictions
  • Our work has produced useful tools with a simple interface that can provide contact predictions to users without requiring a lengthy installation process. (springer.com)
  • In contrast, the regression approach provides a direct and more accurate way to determine a functional relationship matching contact numbers and protein sequence and thus to provide more accurate contact number predictions. (biomedcentral.com)
  • The predictions-20 groups submitted a total of 195 models-were assessed by measuring the recall fraction of water-mediated protein contacts. (nih.gov)
  • Overall the best interface water predictions was achieved by groups that also produced high-quality docking models, indicating that accurate modelling of the protein portion is a determinant factor. (nih.gov)
  • Current ab initio predictions are mainly focused on small proteins. (biomedcentral.com)
  • Most existing tools for predicting DNA-binding specificity in zinc fingers are trained on data obtained from naturally occurring proteins, thereby skewing the predictions. (biomedcentral.com)
  • genome
  • In bacteria a good guide can be gained from genome co-location as interacting proteins tend to be in a common operon but in eukaryotes this simple principle is not sufficient. (biomedcentral.com)
  • In bacteria, the genes of proteins that interact are often co-expressed and found close in the genome sequence on an operon in which all the genes are under common expression control. (biomedcentral.com)
  • Therefore co-location on the genome can provide a good guide to help match pairs of proteins. (biomedcentral.com)
  • To exploit zinc finger proteins for genome manipulation, molecular and structural insights at the binding interface of zinc fingers and corresponding DNA targets are mandatory. (biomedcentral.com)
  • initio
  • If templates are absent from the Protein Data Bank (PDB) library, the models need to be built from scratch, i.e. ab initio folding. (biomedcentral.com)
  • With increasing protein sizes, the conformational phase space of sampling also sharply increases, which makes the ab initio modeling of larger proteins extremely difficult [ 18 ]. (biomedcentral.com)
  • Here, we present an ab-initio method that is based on mutation of the key α-helical residues of individual fingers of the parent template for Zif-268 and its consensus sequence (PDB ID: 1AAY). (biomedcentral.com)
  • pathways
  • Modifying these residues or nucleotides has a large effect on the communication pathways in the protein:RNA complex consistent with kinetic data. (pnas.org)
  • The contribution of each residue or node to the characteristic path length (CPL), defined as an average of the shortest path length between all pairs of nodes in the network, provides an estimate of the effect of node connectivity on communication pathways in a protein. (pnas.org)
  • Like other RTKs, SCF induces dimerization of c-kit followed by trans-autophosphorylation of the cytoplasmic protein tyrosine kinase domain, leading to subsequent recruitment of signaling proteins, tyrosine phosphorylation of substrates, and activation of multiple signaling pathways ( 5 , 6 ). (pnas.org)
  • interact
  • However, given the dominant mechanism of gene duplication and diversification in protein evolution, the more typical situation is that there will be a number of choices (paralogs) for each protein with no guidance from the species name to which pairs of proteins interact. (biomedcentral.com)
  • As extracellular ligands, they interact with specific members of the G-protein-coupled receptor family. (jneurosci.org)
  • Despite years of intense effort, the precise mechanism by which chaperones interact with proteins to enhance their folding is not entirely clear. (elifesciences.org)
  • encodes
  • Here, we report the identification of a Drosophila Pax gene that encodes a protein with only a RED domain and no PAI domain. (pnas.org)
  • simulations
  • In free-energy-based modeling, protein structural populations and dynamics are modeled by computer simulations that satisfy thermodynamic principles, such as detailed balance, on the basis of known interatomic energies. (sciencemag.org)
  • clusters
  • We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. (pnas.org)
  • The average C α -RMSD for all the 16 proteins was 3.8Å in the best of the top five clusters. (biomedcentral.com)
  • nucleotides
  • This study demonstrates that nucleotides in the tRNA as well as residues within the aaRS are essential for information transduction in the protein:RNA complex. (pnas.org)