• Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP. (wikipedia.org)
  • Based on the genome sequencing results, an analysis of structural proteins and prediction of putative microRNAs of Hz-2V was performed. (umass.edu)
  • A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. (iucr.org)
  • Stress-Induced Accumulation of DcAOX1 and DcAOX2a Transcripts Coincides with Critical Time Point for Structural Biomass Prediction in Carrot Primary Cultures (Daucus carota L. (frontiersin.org)
  • Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. (rosettacommons.org)
  • Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
  • Overview over prediction of protein function. (tum.de)
  • Prediction of the effect of single point mutations (sequence variants) on protein function and the organism. (tum.de)
  • As for the first part (Protein Prediction I), the module include an introduction into machine learning with particular focus on how to avoid over-estimating performance. (tum.de)
  • As opposed to the first part (Protein Prediction I), protein structure has only played a minor role: it has been introduced if it has been helpful to further our understanding of function. (tum.de)
  • Students understand the principle concepts in protein sequence analysis with focus on protein function and protein function prediction and are able to evaluate these. (tum.de)
  • Lectures, Seminars, Exercises, Problems for individual and team study: The students apply the theory presented in the lecture by writing a protein function prediction method in the exercise starting from data in varying form (depending on the problem at hand). (tum.de)
  • Because protein structures are more conserved than DNA sequences, and detectable levels of sequence similarity usually imply significant structural similarity. (wikipedia.org)
  • Thus, even proteins that have diverged appreciably in sequence but still share detectable similarity will also share common structural properties, particularly the overall fold. (wikipedia.org)
  • the principal aim of this is to determine whether and to what level does the protein produced by the genetically modified foods have similarity to other known proteins that have the potential of causing allergies among humans and animals. (gmo-safety.eu)
  • This is through the determination of the overall structure of the protein of interest and its similarity to allergens that are known. (gmo-safety.eu)
  • The use of the protein database offers the possibility of determining the similarity of the novel protein of interest with those of allergens that are known on their sequence alignments homology. (gmo-safety.eu)
  • This could also be compared to discrete motifs and domains in the protein where there is complete sequence similarity with that which is present in known allergens, therefore, indicating possibility of shared protein epitopes. (gmo-safety.eu)
  • It belongs to the CD34/Podocalyxin family of sialomucins that share structural similarity and sequence homology. (rndsystems.com)
  • 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)
  • Predicting protein function using structure: structural alignments, structural motifs, annotation transfer via structure similarity. (tum.de)
  • The degree of 3-dimensional shape similarity between proteins. (bvsalud.org)
  • In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity. (nih.gov)
  • We predicted that approximately 15%-30% of all proteins contained transmembrane helices. (rostlab.org)
  • However, we found more proteins with seven transmembrane helices in eukaryotes and more with six and 12 transmembrane helices in prokaryotes. (rostlab.org)
  • Endoglycan, also named Podocalyxin-like 2 protein, is a type I transmembrane glycoprotein. (rndsystems.com)
  • Two transmembrane domains were predicted in p11.7, and a DNA binding motif was found in p31.7 by amino acid sequence analysis, therefore p11.7 and p31.7 were predicted to be envelope and capsid protein, respectively. (umass.edu)
  • Both are transmembrane proteins sharing 30% protein sequence homology in their extracellular domains, but little homology in intracellular domains. (jefferson.edu)
  • Palecek, J. J. & Gruber, S. Kite proteins: a superfamily of SMC/Kleisin partners conserved across bacteria, archaea, and eukaryotes. (nature.com)
  • Structural Insights into the Mechanism of Dynamin Superfamily Proteins. (nih.gov)
  • Two heat-stable globulins constitute 90% of the pulp-derived proteins: beta-conglycinin, which has a molecular weight (MW) of 180,000, and glycinin, which has an MW of 320,000. (medscape.com)
  • However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
  • Characteristic biochemical properties of allergens are that they are proteins or glycoproteins with molecular weights between about 5-100 kDa, which are usually abundant in the food source and often stable to digestion by gastrointestinal enzymes. (usda.gov)
  • Therefore, the present study proposes the three‑dimensional structure of the helicase/protease enzyme of SPONV through homology modeling, using the crystal structure of the Dengue virus‑4 helicase/protease of the same viral family as a template. (spandidos-publications.com)
  • Specific structural features and functional similarities, such as protease activity, have also been associated with both food and inhaled allergens (i.e. pollen, cat, dog, dust mite, etc). (usda.gov)
  • It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. (wikipedia.org)
  • Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. (wikipedia.org)
  • However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different. (wikipedia.org)
  • ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. (nih.gov)
  • By using in silico tools, LipJG3 was related to the transporter protein sequences. (ugm.ac.id)
  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
  • Analysis of the protein sequences of the three CpHsps indicated the presence of 83 amino acids with homology to the a-crystallin domain. (usda.gov)
  • These sequences represent the protein coding region of the Sh2b2 cDNA ORF which is encoded by the open reading frame (ORF) sequence. (genscript.com)
  • Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. (wikipedia.org)
  • These numbers may or may not suggest that there are 1200-2600 folds in the universe of protein structures. (rostlab.org)
  • There are exceptions to the general rule that proteins sharing significant sequence identity will share a fold. (wikipedia.org)
  • For example, a judiciously chosen set of mutations of less than 50% of a protein can cause the protein to adopt a completely different fold. (wikipedia.org)
  • However, such a massive structural rearrangement is unlikely to occur in evolution, especially since the protein is usually under the constraint that it must fold properly and carry out its function in the cell. (wikipedia.org)
  • It would be far better design logic just to put that protein fold into the first cells. (evcforum.net)
  • Considering the widely acknowledged Accordingly, theoretical models of the MG state invariably invoke importance of protein-solvent interactions for stability and fold- a substantial internal hydration20-22. (lu.se)
  • The theory, in this case, is that relative resistance plays a role in inducing allergic responses on condition that the protein of interest possesses allergenic characteristics. (gmo-safety.eu)
  • Some of the immunological properties of allergenic proteins include their ability to stimulate Th-2 type T-cell proliferation, bind serum IgE, elicit a positive prick skin test, and cause histamine and mediator release from mast cells and basophils of sensitive individuals. (usda.gov)
  • Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)
  • Here, I discuss how we - myself, my laboratory and the diffraction community - have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. (iucr.org)
  • The project should involve both studies of protein function by the applicant researchers and structural studies by the PSI:Biology network. (nih.gov)
  • Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. (wikipedia.org)
  • The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. (wikipedia.org)
  • The method of homology modeling is based on the observation that protein tertiary structure is better conserved than amino acid sequence. (wikipedia.org)
  • Because it is difficult and time-consuming to obtain experimental structures from methods such as X-ray crystallography and protein NMR for every protein of interest, homology modeling can provide useful structural models for generating hypotheses about a protein's function and directing further experimental work. (wikipedia.org)
  • Structural and phylogenetic modeling of highly pathogenic avian influenza virus (H5N8), EG-CA285, from migratory birds, Egypt, 2016. (cdc.gov)
  • We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)
  • A pig sperm protein that binds to the extracellular matrix of the egg in a species-specific manner was recently identified and named zonadhesin (Hardy, D. M., and Garbers, D. L. (1995) J. Biol. (embl.de)
  • SH2 (Src Homology 2) is a protein domain found in many intracellular signal-transducing proteins. (nersc.gov)
  • They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)
  • even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). (wikipedia.org)
  • The comparison of the models reveals that the higher stability of HydSL can be attributed to increased inter-subunit electrostatic interactions: the homology models reliably predict that HydSL contains at least five more inter-subunit ion pairs than HupSL. (nih.gov)
  • A team of researchers from Harvard Medical School, using computing resources at the U.S. Department of Energy's National Energy Research Scientific Computing Center (NERSC), have demonstrated a mathematical toolkit that can turn cancer-mutation data into multidimensional models to show how specific mutations alter the social networks of proteins in cells. (nersc.gov)
  • As a result, he was able to generate detailed schematics of how certain mutations altered the vast, complex cellular world of protein social networks-networks that largely determine a cell's health, or lack thereof. (nersc.gov)
  • AlQuraishi found that common and rare mutations are equally likely to affect the protein network. (nersc.gov)
  • Because the mutations do happen, and over deep time, a protein sequence can change quite extensively - to the point that it is no longer the original protein (but structurally similar, nonetheless, and this is what matters). (evcforum.net)
  • Computational design of second-site suppressor mutations at protein-protein interfaces. (rosettacommons.org)
  • SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models. (rosettacommons.org)
  • 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)
  • Following Libdock score screening, the protein-ligand poses were docked using docking optimization (Cdocker) method. (bvsalud.org)
  • The paper I cited describes the structural similarities between ubiquitin and its prokaryotic homologs. (evcforum.net)
  • Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. (iucr.org)
  • Projects may focus on proteins that are the subject of other grant applications, but the specific aims must clearly differ, both with respect to functional studies to be conducted and with respect to the goal of structure determination. (nih.gov)
  • 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)
  • SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
  • A classification by cellular function verified that eukaryotes have a higher proportion of proteins for communication with the environment. (rostlab.org)
  • The current view of protein folding and stability is largely based on SAXS and DLS data13-16 and the extensive exposure of hydropho- a generic structural classification into native (N), compact dena- bic residues suggested by the finding that the heat capacity of the tured or molten globule (MG), and unfolded or denatured (D) MG state is midway between that of the N and D states7 have been conformational states1-10. (lu.se)
  • The results are in accord with the general observation that with increasing temperature, the role of electrostatic interactions in protein stability increases. (nih.gov)
  • Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
  • long range interactions within the protein molecule. (flashcardmachine.com)
  • The motor domain of MYH8 was modeled in order to know what are the interactions altered in the mutant protein. (eurekaselect.com)
  • However, other soy proteins can act as allergens in humans. (medscape.com)
  • This means that taking into consideration the possibility that the transgene produces toxins that are known such as protein allergens. (gmo-safety.eu)
  • Whereas many of the structural characteristics, homology and cross reactivity of food allergens have been explained, specific immunological and biophysical properties of the allergens that contribute to IgE antibody formation are not fully understood. (usda.gov)
  • Due to the structural and biochemical homology between IGF-2 and insulin, elevated levels of IGF-2 can result in hypoglycemia. (medscape.com)
  • Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. (wikipedia.org)
  • For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. (wikipedia.org)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
  • the regions with structural homology covered 20%-30% of all residues. (rostlab.org)
  • SP-4 (residues 192-203), SP-8 (residues 483-494), and SP-10 (residues 668-679) significantly blocked the interaction between S protein and ACE2 by biotinylated enzyme-linked immunosorbent assay, with IC 50 values of 4.30 ± 2.18, 6.99 ± 0.71, and 1.88 ± 0.52 nmol, respectively. (scienceopen.com)
  • Hopfner, K. P. & Tainer, J. A. Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures. (nature.com)
  • Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. (nih.gov)
  • Applicants to this FOA should propose work to solve a substantial biological problem for which the determination of many protein structures is necessary. (nih.gov)
  • Ideally, the solution of these protein structures will also contribute to the understanding of protein sequence-structure relationships in general. (nih.gov)
  • For -lactalbu- min, only water molecules conserved in the human and baboon structures are shown (the structure of the bovine protein has not been reported). (lu.se)
  • Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. (nature.com)
  • Gligoris, T. & Löwe, J. Structural insights into ring formation of cohesin and related SMC complexes. (nature.com)
  • Complexes of Vps34, the sole class III PI3K member, produce PI 3-phosphate (PI(3)P) in the endolysosomal system and during autophagy to regulate vesicle-mediated sorting en route to lysosomes 1 . (nature.com)
  • the calicivirus NTPase was found in membranous replication complexes" /protein_id="NP_786946.1" mat_peptide 2288. (cdc.gov)
  • Homologies were found to 38 of the 113 ORFs predicted for genes with known functions. (umass.edu)
  • Four of structural genes, p11.7, p15.1, p28.4, and p31.7 were identified by matrix assisted laser desorption/ionization time-of-flight mass spectroscopy. (umass.edu)
  • Eukaryotic expression vectors containing genes encoding plant proteins for killing of cancer cells. (weeksmd.com)
  • consequently, genes encoding some of these proteins are being used to design constructs for the inhibition of multiplying cancer cells. (weeksmd.com)
  • Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. (scielo.br)
  • Finally, by successful identification of TNF-induced genes, including MCP-1 (monocyte chemoattractant protein-1), in human monocyrtic leukemia cells ML-1a using a modified differential display technique, we showed that this new technique is a powerful tool in identifying TNF-regulated genes involved in different biological activities. (jefferson.edu)
  • p27 is a protein that binds to and prevents the activation of different G1. (lu.se)
  • The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. (wikipedia.org)
  • X-ray crystallography of OIF and NGF-beta confirmed their structural and sequence homology. (the-scientist.com)
  • Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today's structural biologists. (iucr.org)
  • We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)
  • For each of the CpHsps, the a-crystallin domain was surrounded by divergent N- and C-terminal regions, consistent with the conserved structural features of sHsps. (usda.gov)
  • Taxonomic distribution of proteins containing VWD domain. (embl.de)
  • The complete taxonomic breakdown of all proteins with VWD domain is also avaliable . (embl.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing VWD domain in the selected taxonomic class. (embl.de)
  • Heat map of the average magnitude of interaction energies projected onto a structural representation of SH2 domains (white) in complex with phosphopeptide (green). (nersc.gov)
  • The interaction between the adaptor protein APS and Enigma is involved in actin organisation. (genscript.com)
  • Binding energy were calculated for the protein-ligand poses of lowest -Cdocker Energy and -Cdocker Interaction. (bvsalud.org)
  • Does the transgenic approach employ induce alteration of the level of expression of the proteins that exist in the host crop? (gmo-safety.eu)
  • The proteins should be amenable to high-throughput structure determination and/or should provide suitable targets to motivate new technology development. (nih.gov)
  • NMR structure determination for larger proteins using backbone-only data. (rosettacommons.org)
  • Accurate automated protein NMR structure determination using unassigned NOESY data. (rosettacommons.org)
  • Do the products of the novel gene inserted into plants elicit allergic reactions in humans or animals that are already sensitized to the same protein? (gmo-safety.eu)
  • The third approach is the use of serological techniques to determine whether there are specific IgE antibodies present in the serum of sensitized humans or animals capable of recognizing the protein of interest. (gmo-safety.eu)
  • All soybean proteins and foods currently available for human consumption contain significant amounts of the isoflavones daidzein and genistein, either in the unconjugate form or as different types of glycoside conjugates. (medscape.com)
  • I personally favor the hypothesis that the LUCA was prokaryotic, and not eukaryotic, although some researchers say that the LUCA was more of a eukaryote precisely because of its complexity and the large number of proteins its genome encoded. (evcforum.net)
  • The translated polyprotein consists of three structural [capsid (C), membrane (M) and envelope (E)] and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). (spandidos-publications.com)
  • ALMS1 encodes a ~ 0.5 megadalton protein that localises to the base of centrioles. (springer.com)
  • The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
  • Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
  • Authorities have failed to reach consensus on the risk of feeding allergic or nonallergic infants with soy protein milks. (medscape.com)
  • Species diversity in the structure of zonadhesin, a sperm-specific membrane protein containing multiple cell adhesion molecule-like domains. (embl.de)
  • We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. (nature.com)
  • Structural studies of the D and MG states have naturally focused ed in controversy23. (lu.se)
  • In this work, homology models of both proteins were constructed and analyzed for a number of structural properties. (nih.gov)
  • ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. (nih.gov)
  • There are 25698 VWD domains in 12416 proteins in SMART's nrdb database. (embl.de)
  • Structural basis for phosphotyrosine recognition by the Src homology-2 domains of the adapter proteins SH2-B and APS. (genscript.com)
  • Expression of mouse zonadhesin mRNA is evident only within the testis, and the protein is found exclusively on the apical region of the sperm head. (embl.de)
  • Rattus norvegicus SH2B adaptor protein 2 (Sh2b2), mRNA. (genscript.com)
  • In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. (springer.com)
  • Mammalian bone morphogenetic protein-binding (BMP-binding) endothelial regulator protein. (embl.de)
  • Findings suggest that fibrodysplasia ossificans progressiva maps to band 4q27-31, a region that contains at least 1 gene involved in the bone morphogenic protein (BMP) signaling pathway. (medscape.com)
  • Three Dimensional Structural Modelling of Lipase Encoding Gene from Soil Bacterium Alcaligenes sp. (ugm.ac.id)
  • To understand the structural basis of TPS, we utilize a large number of software packages to estimate how the Arg674Gln mutation would affect the structure and stability of MyH8 gene product. (eurekaselect.com)
  • In this disturbance the maintenance involve the gene expression under the stress either in the form of structural gene or regulatory. (scielo.br)
  • The gene expression of DNA damage inducible protein and DNA damage in response to head DNA % and tail DNA % was protected by Mn-NPs diets. (bvsalud.org)
  • One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
  • Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)
  • The hydration of nonnative states is central to protein folding and stability but has been probed mainly by indirect methods. (lu.se)