Search results for "PDB"

showing 5 items of 15 documents

Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon

2021

18 páginas, 7 figuras, 2 tablas

Models MolecularSalmonella typhimuriumIdentificationSignaling SystemTranscription GeneticTranscription FactorAcademicSubjects/SCI00010Protein ConformationProtein Data Bank (RCSB PDB)ExpressionBiologymedicine.disease_causeRegulonBiofilm Formation03 medical and health sciencesBacterial ProteinsCapsule SynthesisStructural BiologyGeneticsmedicineTranscriptional regulationPhosphorylationPromoter Regions GeneticTranscription factorGene030304 developmental biologyRegulation of gene expression0303 health sciencesMutationBinding Sites030306 microbiologyPromoterGene Expression Regulation BacterialBiología y Biomedicina / BiologíaRepressionCell biologyRegulonEscherichia-Coli K-12MutationGenome BacterialPhosphorelay SystemNucleic Acids Research
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Protein knot server: detection of knots in protein structures

2007

KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…

Models MolecularWeb serverProtein FoldingTheoretical computer scienceProtein ConformationProtein Data Bank (RCSB PDB)MathematicsofComputing_NUMERICALANALYSISAlexander polynomialBiologyBioinformaticscomputer.software_genreUploadUser-Computer InterfaceKnot (unit)Protein structureTheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITYComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATIONGeneticsComputer SimulationSurgical knotsDatabases ProteinInteractive visualizationComputingMethodologies_COMPUTERGRAPHICSInternetQuantitative Biology::BiomoleculesModels StatisticalComputational BiologyProteinsArticlesHaemophilus influenzaeMathematics::Geometric TopologycomputerAlgorithmsSoftwareMathematicsofComputing_DISCRETEMATHEMATICS
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MCC1019, a selective inhibitor of the Polo-box domain of Polo-like kinase 1 as novel, potent anticancer candidate

2019

Polo-like kinase (PLK1) has been identified as a potential target for cancer treatment. Although a number of small molecules have been investigated as PLK1 inhibitors, many of which showed limited selectivity. PLK1 harbors a regulatory domain, the Polo box domain (PBD), which has a key regulatory function for kinase activity and substrate recognition. We report on 3-bromomethyl-benzofuran-2-carboxylic acid ethyl ester (designated: MCC1019) as selective PLK1 inhibitor targeting PLK1 PBD. Cytotoxicity and fluorescence polarization-based screening were applied to a library of 1162 drug-like compounds to identify potential inhibitors of PLK1 PBD. The activity of compound MC1019 against the PLK1…

PBD Polo box domainMTD maximal tolerance doseCDC25 cell division cycle 25HIF-1α hypoxia-inducible factor 1 αMST microscale thermophoresisIC50 50% inhibition concentrationMFP M phase promoting factorPARP-1 poly(ADP-ribose) polymerase-10302 clinical medicineFOXO forkhead box ONec-1 necrostatin 1CDC2 cell division cycle protein 2 homologGeneral Pharmacology Toxicology and PharmaceuticsMitotic catastropheCDK cyclin-dependent kinase0303 health sciencesChemistryPolo-like kinaseMono-targeted therapyCell cycleBUBR1 budding uninhibited by benzimidazole-related 1Polo box domain030220 oncology & carcinogenesisPLK1 Polo-like kinaseNecroptosisSpindle damagePLK1IHC immunohistochemistryOriginal articleNecroptosisCell cyclePLK1APC/C anaphase-promoting complex/cyclosomePLK3ABC avidin-biotin complexPI propidium iodide03 medical and health sciencesFBS fetal bovine serumPDB Protein Data BankKd the dissociation constantKinase activity030304 developmental biologyAkt/PKB signaling pathwayCell growthlcsh:RM1-950LC3 light chain 3lcsh:Therapeutics. PharmacologyCancer researchDAPKs death-associated protein kinase3-MA 3-methyladenineDAPI 4′6-diamidino-2-phenylindoleSAC spindle assembly checkpointActa Pharmaceutica Sinica B
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RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

2020

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new lev…

Repetitive Sequences Amino AcidAcademicSubjects/SCI00010BiologíaStatistics as TopicProtein Data Bank (RCSB PDB)Computational biologyBiologyRepetitive SequencesGene Ontology; HEK293 Cells; HeLa Cells; Humans; Proteins; Reproducibility of Results; Statistics as Topic; User-Computer Interface; Databases Protein; Repetitive Sequences Amino Acid; Tandem Repeat SequencesDatabases03 medical and health sciencesAnnotationUser-Computer InterfaceProtein structureSimilarity (network science)Tandem repeatGeneticsDatabase IssueHumansDatabases ProteinCiencias Exactasdatabase030304 developmental biology0303 health sciencesHierarchy (mathematics)Protein030302 biochemistry & molecular biologyProteinsReproducibility of Resultscomputer.file_formatProtein Data BankClass (biology)proteinsAmino AcidComputingMethodologies_PATTERNRECOGNITIONGene OntologyHEK293 CellsclassificationTandem Repeat Sequencesprotein tandem repeat structures[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]computerHeLa CellsNucleic Acids Research
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Local vs global motions in protein folding

2013

It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respect…

biologyChemistryBinding proteinProtein Data Bank (RCSB PDB)NanotechnologyForce field (chemistry)ArticleComputer Science ApplicationsWW domainMolecular dynamicsForminsPrincipal component analysisbiology.proteinProtein foldingPhysical and Theoretical ChemistryBiological system
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