• Reverse transcription quantitative PCR results demonstrated high expression of an actin-binding Rho-activating protein in the latter stages of virus-infected cells, and molecular docking, cell transfection and coimmunoprecipitation experiments confirmed that it interacted with the ORF55 protein. (biomedcentral.com)
  • By employing this information, molecule libraries can be filtered for subsequent affinity assays and molecular structures can be refined with regard to affinity and selectivity. (uni-marburg.de)
  • The predicted docking structures of atrolysin C and TIMPs were submitted to molecular dynamics simulations and the complex atrolysin C/N-TIMP-3 was the only one that maintained the inhibitory conformation. (ox.ac.uk)
  • The tertiary structure was elucidated using the 1EX9 lipase from Pseudomonas aeruginosa PAO1 as a template and molecular docking was executed with three substrates. (edu.pe)
  • Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet. (keywen.com)
  • HQSAR Hologram QSAR (HQSAR) uses molecular holograms and PLS to generate fragment-based structure-activity relationships. (keywen.com)
  • SciVision - Databases , molecular modeling , and structure-activity relationship software for Windows. (keywen.com)
  • Crystal and molecular structure determination. (keywen.com)
  • The mdxvu program is a molecular dynamics and molecular structure analysis code. (keywen.com)
  • The Proceedings of this conference have recently been published in the Journal of Molecular Structure (THEOCHEM) vol 368. (keywen.com)
  • On the basis of our results, a molecular model of peptide-bound NPRA was developed by homology modeling with the C-type natriuretic peptide- (CNP-) bound natriuretic peptide receptor C (NPRC) crystal structure. (hal.science)
  • 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)
  • Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny. (genomyx.ch)
  • an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles. (sbgrid.org)
  • SEquence-structure alignment with 123D+ server. (keywen.com)
  • The structure of the molecules can be incorporated in the alignment. (keywen.com)
  • The input to the program was the alignment between the target sequence and template structure(s). (keywen.com)
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. (keywen.com)
  • Evaluates Multiple Sequence Alignment using structural information with APDB and iRMSD. (crg.eu)
  • The structure suggests that the KaiB binding site is covered in the dimer interface of the KaiA "closed" conformation, observed in the crystal structure, which suggests an allosteric regulation mechanism. (ox.ac.uk)
  • Differences in the observed inhibitor conformation between the yeast and human structures are caused by differing residues in the binding pocket. (duke.edu)
  • Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure, and improving state-of-the-art features for long-range contact prediction. (biorxiv.org)
  • c) combination of pretraining features and classical features for secondary structure and contact prediction. (biorxiv.org)
  • Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. (biomedcentral.com)
  • The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported. (biomedcentral.com)
  • Protein and peptide interaction prediction and dot-blot overlay assay confirmed that peptides identified by phage display could interact with the ORF55 protein. (biomedcentral.com)
  • Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
  • Of the variety of methods to be used for tertiary structure prediction, we choose homology modeling as a first approach to our goal. (tu-muenchen.de)
  • Protein secondary structure prediction based on position-specific scoring matrices. (keywen.com)
  • Structure drawing, 3D modeling and NMR prediction. (keywen.com)
  • Prime Prime is a fully-integrated protein structure prediction program. (keywen.com)
  • Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. (biomedcentral.com)
  • Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction. (biomedcentral.com)
  • Nonetheless, it is common knowledge that RNA 3D structure is more conserved than RNA sequence and that such principle could be used for comparative RNA structure prediction in a similar way it is done for proteins [ 11 ]. (biomedcentral.com)
  • IL-22BP also shares homology with other related cytokine receptors IL-10RB, and IL-20RA. (wikipedia.org)
  • 4 , 5 , 6 We present a pipeline for the identification and characterization of distant homologs and apply it to 7-transmembrane-domain ion channels (7TMICs), a protein group founded by insect odorant and gustatory receptors. (genomyx.ch)
  • Nucleotide sequences of PCR amplicons showed 99%-100% similarity to IHHNV isolates from Latin America and Asia. (cdc.gov)
  • 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)
  • Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. (genomyx.ch)
  • Although the function of YegS is not definitively known, it has been annotated as a potential diacylglycerol or sphingosine kinase based on sequence similarity with eukaryotic enzymes of known function. (ox.ac.uk)
  • For this set of datasets we used the webservice of sequence similarity search provided by the pdb called PDBeXplore, which can be accessed here . (tu-muenchen.de)
  • contains two structures with a very high similarity, with is due to the fact, that the structure is that of the original protein in different states. (tu-muenchen.de)
  • The structure of murine leukemia inhibitory factor (LIF) has been determined by X-ray crystallography at 2.0 A resolution. (ox.ac.uk)
  • These techniques are replacing x-ray crystallography for the determination of protein structure. (keywen.com)
  • The learned representation space has a multi-scale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. (biorxiv.org)
  • Sequence alignments for the functionally related molecules oncostatin M and ciliary neurotrophic factor, when mapped to the LIF structure, indicate regions of conserved surface character. (ox.ac.uk)
  • a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. (sbgrid.org)
  • Sequence-structure alignments Sequence-structure alignments were generated and tested both at the sequence level as well as at the 3D level. (keywen.com)
  • Interleukin-22 receptor subunit alpha-2 (IL-22RA2), also known as interleukin-22 binding protein (IL-22BP) is a naturally secreted monomeric protein acting as an interleukin-22 (IL-22) antagonist with inhibitory effects on IL-22 activity in vivo. (wikipedia.org)
  • This homology extends to the secondary and tertiary structure of the proteins allowing specific binding and protein-protein interactions. (wikipedia.org)
  • To elucidate the ligand-binding surface of the CC chemokine-binding proteins Evasin-1 and Evasin-4, produced by the tick Rhipicephalus sanguineus, we sought to identify the key determinants responsible for their different chemokine selectivities by expressing Evasin mutants using phage display. (unige.ch)
  • The results also suggest that phage display may offer a useful approach for rapid investigation of the pharmacophores of small inhibitory binding proteins. (unige.ch)
  • In this report, we reveal an important function for ARD1 in mammalian cells as a protein acetyltransferase by direct binding to HIF-1alpha to regulate its stability. (nih.gov)
  • In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)
  • Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. (uni-marburg.de)
  • Binding sites of other proteins which are similar to the binding site of the target protein can offer hints for possible side effects of a new drug prior to clinical studies. (uni-marburg.de)
  • 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)
  • The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
  • 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)
  • The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria. (uni-marburg.de)
  • The crystal structure and biological function of leukemia inhibitory factor: implications for receptor binding. (ox.ac.uk)
  • A model for receptor binding based on the structure of the GH ligand-receptor complex requires additional, novel features to account for these data. (ox.ac.uk)
  • The papillomaviral DNA replication initiation protein E1 has origin recognition and ATP-dependent DNA melting and helicase activities, and it consists of a DNA-binding domain and an ATPase/helicase domain. (cshl.edu)
  • Here we present the crystal structure of the monomeric HPV-18 E1 DNA-binding domain refined to 1.8-A resolution. (cshl.edu)
  • This gene may represent a mammalian heterochromatic gene, encoding a putative RNA-binding protein similar to the yeast Luc7p subunit of the U1 snRNP splicing complex that is normally required for 5' splice site selection. (ox.ac.uk)
  • We demonstrate that the protein has low cation specificity and contains multiple binding sites able to chelate divalent and trivalent metals with low affinity. (cnr.it)
  • The C-terminal domain of the 990-amino acid Schizosaccharomyces pombe Spt5 protein, composed of repeats of a nonapeptide motif (consensus sequence TPAWNSGSK), is necessary and sufficient for binding to the capping enzymes in vivo (in a two-hybrid assay) and in vitro. (mskcc.org)
  • Crystal structure of proflavine, a DNA binding agent. (keywen.com)
  • We have also identified the cleft and cavities in these structures and have explored the potential binding sites. (ijpsr.com)
  • Our first structure shows an H3-H4 tetramer bound by two MCM2 histone-binding domains (HBDs), which hijack interaction sites used by nucleosomal DNA. (cornell.edu)
  • Therefore, binding to H3K27me3 is essential for LHP1 protein function. (uzh.ch)
  • 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)
  • Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). (embl.de)
  • A number of actin-binding proteins, including spectrin, alpha-actinin and fimbrin, contain a 250 amino acid stretch called the actin binding domain (ABD). (embl.de)
  • Advanced spectroscopic techniques for structure and determination in organic chemistry . (keywen.com)
  • Structure determination and refinement of human alpha class glutathione transferase A1-1. (keywen.com)
  • Moreover, these proteins' remarkable sequence dissimilarity made it uncertain whether disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF, and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. (genomyx.ch)
  • Their work concluded that the overall structural changes between two homologous proteins were proportional to their sequence differences. (biomedcentral.com)
  • It was then estimated that homologous proteins aligning with less than 20% sequence identity could have large structural differences [ 14 ]. (biomedcentral.com)
  • Distinguishing three-dimensional structures characteristically formed by homologous protein sequences. (bvsalud.org)
  • It also includes the study of existing drugs, their biological properties, and their quantitative structure-activity relationships (QSAR). (keywen.com)
  • However, to date no general large-scale study has systematically addressed the quantitative analysis of the relationship between sequence and structure conservation in RNA molecules. (biomedcentral.com)
  • The quantitative evaluation of protein structure quality was verified with Volume Area Dihedral Angle Reporter server. (uni-mysore.ac.in)
  • Diagnosis of Lassa fever has also advanced from basic serological tests to more sophisticated methods such as quantitative real time polymerase chain reaction (qRT-PCR) and sequencing, which are particularly useful for identifying outbreak strains. (bvsalud.org)
  • Based on an established filtering strategy and data analyses, along with confirmation by Sanger sequencing and co‑segregation, a novel frameshift mutation c.1317delA (p.Ala440LeufsTer14) in exon 10 of the APC gene was identified. (spandidos-publications.com)
  • To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. (biorxiv.org)
  • Rhodanese homology domains are structural modules of about 120 amino acids, which occur in the three major evolutionary phyla [ 9 ]. (expasy.org)
  • It was back in the eighties when Chothia and Lesk first quantified such evolutionary relationship for proteins [ 12 - 14 ]. (biomedcentral.com)
  • Comparing the peptides to the National Center for Biotechnology Information database revealed four potential interacting proteins. (biomedcentral.com)
  • PDT allows a direct link and identification between a large number of random peptides and DNA-coding sequences. (biomedcentral.com)
  • 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)
  • Thus although the bioinformatics analysis and structure of YegS indicate that many of the ligand recognition determinants for lipid kinase activity are present, the absence of such activity may be due to specificity for a different lipid substrate or the requirement for activation by an, as yet, undetermined mechanism. (ox.ac.uk)
  • The Cdc25 family of protein dual specificity phosphatases (EC 3.1.3.48 ). (expasy.org)
  • The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. (biomedcentral.com)
  • Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis , and 708 protein structures and 7391 protein interactions for L. infantum . (biomedcentral.com)
  • During viral infection, the ORF55 protein exerts its biological function through interactions with host proteins. (biomedcentral.com)
  • Protein-protein interactions (PPIs) play essential roles in many biological processes. (nature.com)
  • Identification of protein-protein interactions (PPIs) is important for understanding how proteins work together in a coordinated fashion in a cell to perform cellular functions. (nature.com)
  • Even for Arabidopsis , known PPI data cover interactions with only about 34.55% of proteins. (nature.com)
  • Several methodologies, capable of handling and generating large-scale protein interaction data, have been employed, such as the experimental techniques of yeast two-hybrid and affinity purification coupled with mass spectrometry [ 17 ]. (biomedcentral.com)
  • Although the enzyme is highly conserved amongst animals, only the yeast enzyme structure is available for rational drug design. (duke.edu)
  • This C-terminal truncation led to the determination of the human ACC2 CT domain-CP-640186 complex crystal structure, which revealed distinctions from the yeast-enzyme complex. (duke.edu)
  • When expressed as a recombinant protein in transfected cells, PV 3A cofractionates with endoplasmic reticulum markers ( 66 ), and its single transient expression can disrupt the secretory apparatus ( 23 ) and decrease major histocompatibility complex (MHC) class I expression ( 22 ). (asm.org)
  • Initial studies demonstrated that rabbit antimouse type VII collagen antibodies, as well as rabbit antibodies raised against human recombinant protein type VII collagen, were able to induce blisters in mice. (medscape.com)
  • For this purpose, lip gene was amplified by conventional Polymerase Chain Reaction (PCR) and nucleotide sequence was analyzed in silico. (edu.pe)
  • In the present study, we analysed the nonsynonymous single nucleotide polymorphism of GATA4, which are involved in congenital heart disease by predicting the changes in protein structures. (uni-mysore.ac.in)
  • To understand the role of nonsynonymous single nucleotide polymorphisms, we mutated the sequence and translated into amino acids. (uni-mysore.ac.in)
  • Phylogenetic analysis using capsid gene and whole-genome sequences demonstrated that the isolates clustered with an IHHNV isolate from Ecuador. (cdc.gov)
  • A foreign protein is first expressed in fusion with one of the phage capsid proteins by cloning the foreign DNA sequence in frame with the gene encoding the chosen capsid protein [ 22 ]. (biomedcentral.com)
  • 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)
  • 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)
  • Purified CyHV-2 ORF55 protein was obtained by prokaryotic expression, and the interacting peptide was screened out using phage display. (biomedcentral.com)
  • Various stress response proteins (heat shock, phage shock, cold shock) from all phyla. (expasy.org)
  • There is a strong emphasis on the structure of molecules, particularly proteins, which are the nanoscale machines that carry out most processes in living organisms. (bbk.ac.uk)
  • The nature of the chemical bond and the structure of molecules and crystals. (uni-marburg.de)
  • Structure: an assortment of carbon molecules in a non-crystalline, irregular, glassy state. (keywen.com)
  • KGNMOL, ab initio electronic structure calculations for large molecules. (keywen.com)
  • The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. (biomedcentral.com)
  • Similar to proteins, functional RNA molecules fold into specific three-dimensional conformations essential for performing their biological activity. (biomedcentral.com)
  • The accessory gene regulator ( agr ), a well-studied QS system, controls the expression of a series of virulence-associated protein genes in some Gram-positive bacteria 19, 20 . (ijpsr.com)
  • Five Dmrt family genes with full-length transcript sequences were identified in Amur sturgeon. (researchsquare.com)
  • One candidate protein that could be involved in PRC1-like functions in plants is LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), because LHP1 associates with genes marked by H3K27me3 in vivo and has a chromodomain that binds H3K27me3 in vitro . (uzh.ch)
  • In spite of this similar organization, the SARS-CoV RNA sequence is only distantly related to that of previously characterized coronaviruses ( 9 ). (cdc.gov)
  • IL-22BP is a soluble monomeric cytokine receptor protein. (wikipedia.org)
  • The full-length viral genome sequence was similar to those derived from the Hong-Kong Hotel M isolate. (cdc.gov)
  • In addition, we have completely sequenced the viral genome of the SARS-CoV HSR1 and compared it to other SARS-CoV strains recently isolated in disease-epidemic areas. (cdc.gov)
  • 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)
  • The study aimed to explore the protein coding ability of the pri-miR156a in Brassicaceae plants using bioinformatics analysis of the available proteomes and translatomes reported for Arabidopsis thaliana. (fortunepublish.com)
  • This study is the first to shed light on the structural determinants required for the interaction between a SVMP and a TIMP, and suggests a structural basis for TIMP-3 inhibitory action and related proteins such as the ADAMs. (ox.ac.uk)
  • IL-22BP is a secreted protein that lacks both transmembrane and intracellular domains, it contains two tandem fibronectin-III domains, glycosylation sites and four conserved cysteine residues. (wikipedia.org)
  • However, both proteins appear to target chemokine N termini, presumably because these domains are key to receptor signaling. (unige.ch)
  • Finally, we note that sequence diversity in chromo domains may lead to diverse functions in eukaryotic gene regulation. (ox.ac.uk)
  • The 2.0-A structure of KaiA of S. elongatus reported here shows that the protein is composed of two independently folded domains connected by a linker. (ox.ac.uk)
  • is composed of two domains which, in spite of a negligible sequence homology, are characterized by very similar three dimensional folds. (expasy.org)
  • Rhodanese-like proteins are either composed of a single catlytic rhodanese domain, as found in glpE, or composed of two rhodanese domains, with the C-terminal domain displaying the putative catalytic Cys as observed in Rhobov and rhdA. (expasy.org)
  • Rhodanese domains, either catalytic or inactive (i.e. where the active-site Cys is replaced by another residue), are also found associated with other protein domains such as MAPK-phosphatases or thiL, an Escherichia coli enzyme involved in thiamin and thiouridine biosynthesis. (expasy.org)
  • however, little is known about the structures of the A and E domains. (jneurosci.org)
  • There are 66728 CH domains in 45684 proteins in SMART's nrdb database. (embl.de)
  • IL-22BP shares approximately 34% sequence homology with the extracellular domain of one subunit of the heterodimeric membrane-bound IL-22R, which is the main cellular receptor for IL-22 providing the subsequent signalling. (wikipedia.org)
  • Atrolysin C is a P-I snake venom metalloproteinase (SVMP) from Crotalus atrox venom, which efficiently degrades capillary basement membranes, extracellular matrix, and cell surface proteins to produce hemorrhage. (ox.ac.uk)
  • The last dataset from HHPred contains five structures which only decend from bacteria with only one of the structures has a direct connection with PheOH as this one binds L-Phe. (tu-muenchen.de)
  • Tertiary structures of AgrA proteins of some pathogenic bacteria like Listeria monocytogenes, Chlamydia trachomatis, Enterococcus faecalis, Streptococcus pyogenes and Macrococcus canis showing antimicrobial resistance are not yet available in structural databases like PDB. (ijpsr.com)
  • The compositional and structural differences of the LytTR domain of AgrA proteins between the pathogenic and non-pathogenic bacteria were analyzed in our study. (ijpsr.com)
  • Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
  • Sequence determination and homology modeling of lipase from Marinobacter sp. (edu.pe)
  • Profundice en los temas de investigación de 'Sequence determination and homology modeling of lipase from Marinobacter sp. (edu.pe)
  • Forum for 3D macromolecular structure determination. (keywen.com)
  • This is a general concern since the methods for determination of three dimensional structure of a protein are time consuming and expansive. (ijpsr.com)
  • Syroegin, E. A. , Aleksandrova, E. V. , and Polikanov, Y. S. (2022) Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes . (cornell.edu)
  • As one of the two distinct complexes, namely, Polycomb Repressive Complex 1 (PRC1) and PRC2, PRC2 mediates gene silencing by modulating chromatin structure [ 2 ]. (hindawi.com)
  • We first designed alanine mutants based on the Evasin-1·CCL3 complex structure and an in silico model of Evasin-4 bound to CCL3. (unige.ch)
  • The modeled proteins were validated by several methods, and the physico-chemical properties of these refined protein structures were predicted using in-silico methods. (ijpsr.com)
  • The structure reveals that the dimerization helix is significantly different from that of bovine papillomavirus type 1 (BPV-1). (cshl.edu)
  • A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. (nature.com)
  • Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum . (biomedcentral.com)
  • Polycomb Group (PcG) proteins are a family of protein complex that regulate gene expression, especially repressing gene transcription [ 1 ]. (hindawi.com)
  • Selected variants were then produced as purified proteins and characterized by surface plasmon resonance analysis and inhibition of chemotaxis. (unige.ch)
  • Analysis of 2179 clonal sequences derived from hypervariable region 1 (HVR1) of the HCV genome in samples obtained from patients with acute (n = 49) and chronic (n = 102) HCV infection showed that intra-host HVR1 diversity was 1.8 times higher in patients with chronic than acute infection. (iospress.com)
  • Sequence analysis of the complete genome of SARS-CoV has shown an RNA molecule of about 29,750 bases in length, with a genome organization similar to that of other coronaviruses ( 9 - 11 ). (cdc.gov)