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  • predict
  • In this study, we present DeepSacon, a computational method that can effectively predict protein solvent accessibility and contact number by using a deep neural network, which is built based on stacked autoencoder and a dropout method. (biomedcentral.com)
  • During the past few years, there are numerous studies focused on developing computational methods to predict contact number in the protein sequence. (biomedcentral.com)
  • exposure
  • In the past, several methods for predicting protein solvent accessible surface area have been implemented mostly in a discrete fashion as the two-state or three-state classification of the exposure rate of residues. (biomedcentral.com)
  • fragments
  • Recently, researchers from Nexia Biotechnologies , in cooperation with the Materials Science Team of the U.S. Army, described the successful synthesis of fibers spun from a solution of proteins obtained by transferring fragments of the corresponding spider gene into suitable mammalian cells. (tms.org)
  • eukaryotic
  • Since the number of related copies for eukaryotic proteins tends to be smaller, there are fewer proteins to compare and it is therefore harder to detect 'covariation' when it occurs. (elifesciences.org)
  • Since being recognized in these three eukaryotic transcription factors, PAS domains have been found in proteins from all three kingdoms of life that perform functions as diverse as DNA binding, phosphorylation, ion conduction, and others ( , 1 ). (pnas.org)
  • Roles
  • RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. (biomedcentral.com)
  • The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. (biomedcentral.com)
  • molecules
  • Proteins are considered the 'workhorse molecules' of life and they are involved in virtually everything that cells do. (elifesciences.org)
  • Proteins must have the correct shape to function properly, as they often work by binding to other proteins or molecules-much like a key fitting into a lock. (elifesciences.org)
  • DNA contains the instructions required to make proteins and other molecules in cells. (elifesciences.org)
  • Thus, the creation of collections of specific binding molecules targeting a great number of individual proteins, including variants and modifications, will become equally important ( 4 ). (pnas.org)
  • enzymatic activity
  • The best characterized of all RNRs is the class Ia enzyme from Escherichia coli that employs a di-iron-tyrosyl-radical cofactor to initiate chemistry and requires two dimeric protein subunits for enzymatic activity. (elifesciences.org)
  • fluorescence
  • The contribution of individual Trp residues to alpha-actin fluorescence was evaluated by means of an analysis of their microenvironment, which was done on the basis of PIR-International protein sequence database information. (semanticscholar.org)
  • Motifs
  • The fact that most known ER export motifs are not active when transferred to reporter proteins suggests that optimal recruitment of membrane proteins by the COPII budding machinery is controlled by multiple determinants. (biologists.org)
  • correlate
  • We here describe an updated analysis of the epiplasmin family of the ciliate P. tetraurelia , which regroups 51 proteins and attempt to correlate protein structure information obtained from Hydrophobic Cluster Analysis (HCA) [ 10 ] with both gene expression level and similarity tree analysis. (biomedcentral.com)
  • electron
  • Improved methods for building protein models in electron density maps and the location of errors in these models. (psu.edu)
  • chemistry
  • Despite the diverse chemistry, we demonstrate that the proteins are evolutionarily related and that only a limited set of amino acid changes in the active sites are responsible for the switch in chemistry. (pnas.org)
  • suggests
  • The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns. (rsc.org)
  • contrast
  • In contrast to this rich body of work for monomeric proteins, relatively little is known about the utility of such statistical models in predicting protein-protein interactions. (elifesciences.org)
  • The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. (rsc.org)
  • pairs
  • As such, when pairs of interacting proteins from different species are compared, there will be many positions in the two proteins that vary. (elifesciences.org)
  • However, conservation does not provide mutual information between interacting partners so as to identify the residue pairs in contact. (pnas.org)
  • important
  • Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. (rsc.org)
  • Our findings significantly expand the repertoire of reactions reported for this important protein family and provide an illustrative example of enzyme evolution. (pnas.org)
  • In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation. (springer.com)
  • We show that this set of proteins handles an important developmental information in Paramecium since maintenance of epiplasm organization is crucial for cell morphogenesis. (biomedcentral.com)
  • As higher order interactions make significant contribution to the potential energy landscape of folded proteins, it is important to identify them to estimate their contributions to the overall stability of a protein structure. (scienceexchange.com)
  • approaches
  • Some experimental techniques such as X-ray crystallography, NMR Spectroscopy and cross-linking approaches, have applied to investigate protein-RNA interface properties. (biomedcentral.com)
  • Chemical approaches towards understanding protein functions. (brandeis.edu)
  • combinations
  • Combinations of inter- and intramolecular interactions hold the cell machineries and govern the flow of information transmitted through cell signaling pathways. (pnas.org)
  • Mechanism
  • This article reveals an autonomous mechanism of inhibition relief for class III Fic proteins, which hinges on autoadenylylation of an inhibitory helix. (pnas.org)
  • efficiently
  • Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact. (pnas.org)
  • pairwise
  • According to the earlier studies (14), if we approximate each residue as a sphere centred on its location, it is possible for a maximum of four closely packed spheres to make mutual contact, thus giving rise to pairwise, triplet and quadruple interactions. (scienceexchange.com)