Improved FlexX Docking Using FlexS-Determined Base Fragment Placement

2005 ◽  
Vol 45 (4) ◽  
pp. 993-1001 ◽  
Author(s):  
Simon S. J. Cross
Keyword(s):  
Base Fragment ◽  
Flexx Docking

scholarly journals Short-term time series prediction based on sceleton algebraic sequences with internal smoothing

2012 ◽  
Vol 53 ◽  
Author(s):  
Rita Palivonaitė ◽  
Minvydas Ragulskis
Keyword(s):  
Time Series ◽  
Real World ◽  
Numerical Experiments ◽  
Time Series Prediction ◽  
Forecast Method ◽  
Short Term ◽  
Forecasting Method ◽  
Base Fragment

An improved algebraic forecasting method with internal smoothing is proposed for short-term time series prediction. The concept of the H-rank is proposed for the detection of a base fragment of the sequence. Numerical experiments with artificially generated and real-world time series are used to illustrate the forecast method.

scholarly journals Acid selective pro-dye for cellular compartments

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Barbara Czaplińska ◽  
Katarzyna Malarz ◽  
Anna Mrozek-Wilczkiewicz ◽  
Robert Musiol
Keyword(s):  
Theoretical Calculations ◽  
Bond Cleavage ◽  
Stokes Shift ◽  
Fluorescent Properties ◽  
Fluorescent Compound ◽  
Biological Assays ◽  
Selective Staining ◽  
Base Fragment ◽  
Imine Bond ◽  
Cellular Compartments

Abstract A novel pro-dye approach for the acid-selective staining of the subcellular compartments for better permeability and selectivity was applied. The designed sensor has suitable physicochemical properties such as a large Stokes shift and a long-lived intracellular fluorescence. The Schiff base fragment was used for the acid-sensitive release of a fluorophore without affecting the overall stability of the biological systems. Due to the presence of an imine bond in its structure and its unique fluorescent properties, it can be presented as a “pro-dye” for acidic structures such as lysosomes. As a result of an imine bond cleavage, a new fluorescent compound is released, whose substantially shifted excitation and emission wavelengths enable a more selective and effective imaging of lysosomes and endosomes. The presented report provides the chemical, physicochemical and optical profiles as well as biological assays and theoretical calculations.

scholarly journals A tetranuclear cubane-like nickel(II) complex with a tridentate salicylideneimine Schiff base ligand: tetrakis[μ3-4-methyl-N-(2-oxidophenyl)salicylideneiminato]tetrakis[methanolnickel(II)] methanol 0.8-solvate

2016 ◽  
Vol 72 (12) ◽  
pp. 1776-1779
Author(s):  
Gordana Pavlović ◽  
Mihael Majer ◽  
Marina Cindrić
Keyword(s):  
Hydrogen Bond ◽  
Schiff Base ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Site Occupancy ◽  
Schiff Base Ligands ◽  
Base Fragment ◽  
Crystal Complex ◽  
Additional Stabilization ◽  
A Site

The tetranuclear title complex, [Ni4(C14H11NO2)4(CH3OH)4]·0.8CH3OH, has a distorted cubane topology shaped by four Schiff base ligands. The cubane [Ni4(μ3-O4)] core is formedviathe O atoms from the Schiff base ligands. The octahedrally coordinated NiIIions occupy alternating vertices of the cube. Each NiIIion is coordinated by oneO,N,O′-tridentate dianionic ligand, two O atoms of oxidophenyl groups from adjacent ligands and the O atom of a coordinating methanol molecule. The cubane core is stabilizedviaan intramolecular O—H...O hydrogen bond between the hydroxy group of the coordinating methanol molecules and the phenolate O atom of the aldehyde Schiff base fragment. Additional stabilization is obtainedviaintramolecular C—H...O hydrogen bonds involving aromatic C—H groups and the oxygen atoms of adjacent methanol molecules. In the crystal, complex molecules are linked into chains parallel to thecaxisviaweak C—H...O hydrogen bonds. The partial-occupancy disordered methanol solvent molecule has a site occupancy of 0.8 and is linked to the tetranuclear unitviaan intermolecular C—H...O hydrogen bond involving a phenolate O atom.

scholarly journals Transcriptional regulation of the T cell antigen receptor zeta subunit: identification of a tissue-restricted promoter.

1994 ◽  
Vol 180 (4) ◽  
pp. 1529-1534 ◽  
Author(s):  
B L Rellahan ◽  
J P Jensen ◽  
A M Weissman
Keyword(s):  
T Cell ◽  
Transcription Initiation ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
Antigen Receptors ◽  
Unique Role ◽  
Tissue Specific ◽  
Cell Antigen ◽  
Tissue Specific Promoter ◽  
Base Fragment

The cell surface expression of T cell antigen receptors (TCR) is regulated in part by the limiting synthesis of the zeta subunit. Utilizing fragments from the 5' region of the human zeta gene, two discrete regions that promote transcription were characterized. Both of these elements are located within 125 bases of the most 3' site of transcription initiation. The more proximal (3') promoter exhibits activity in lymphoid as well as nonlymphoid cells. In contrast, the more distal (5') promoter element functions in a tissue-restricted fashion. The tissue-specific promoter is localized to a 29-base fragment. The sequence of this region is remarkable for a stretch of 11 consecutive purines that are required for activity. This element constitutes the only known tissue-specific promoter for an invariant TCR subunit. Consistent with the unique role served by the zeta subunit in assembly of the TCR, this study demonstrates that the expression of the zeta gene is regulated in a fashion distinct from other TCR components.

scholarly journals Algebraic time series forecasting and segmentation models

2015 ◽  
Vol 56 ◽  
Author(s):  
Kristina Lukoševičiūtė ◽  
Rita Palivonaitė
Keyword(s):  
Time Series ◽  
Real World ◽  
Numerical Experiments ◽  
Financial Time Series ◽  
Time Series Forecasting ◽  
Segmentation Method ◽  
Financial Time ◽  
Base Fragment ◽  
Segmentation Models

An algebraic segmentation method based on algebraic predictor with internal smoothing is proposed. The concept of the rank of the sequence is proposed for the detection of a base fragment of the sequence. Numerical experiments with a real-world financial time series illustrate the segmentation method.

Mass spectra of isosteviol derivatives: I. Fragmentation of isosteviol derivatives having a Schiff base fragment on C4 under electron impact

2009 ◽  
Vol 79 (11) ◽  
pp. 2377-2382 ◽  
Author(s):  
R. Z. Musin ◽  
V. M. Babaev ◽  
I. Yu. Strobykina ◽  
V. E. Kataev ◽  
V. I. Gavrilov ◽  
...  
Keyword(s):  
Schiff Base ◽  
Electron Impact ◽  
Mass Spectra ◽  
Base Fragment

Substitution at Phenyl Rings of Chalcone and Schiff Base Moieties Accounts for their Antiproliferative Activity

2019 ◽  
Vol 19 (5) ◽  
pp. 620-626 ◽  
Author(s):  
Marwa S. Salem ◽  
Rasha A. Hussein ◽  
Wael M. El-Sayed
Keyword(s):  
Schiff Base ◽  
Schiff Bases ◽  
Antiproliferative Activity ◽  
Phenyl Ring ◽  
Structural Similarity ◽  
Active Member ◽  
Chlorine Substitution ◽  
Phenyl Rings ◽  
Base Fragment ◽  
Induced Apoptosis

Background: In a continuous combat against cancer, which is one of the leading causes of mortality now, chalcone and Schiff bases moieties have been incorporated and their antiproliferative activities and associated mechanisms against liver (HepG2) and breast (MCF-7) cell lines in addition to normal fibroblasts (WI-38) have been examined. Methods: Derivatives 4 and 5 of Schiff bases only and chalcone derivatives of Schiff bases 1 and 2 were devoid of any antiproliferative activity. All three compounds (3, 6, and 7) with significant antiproliferative activity were selective and caused no growth inhibition in normal fibroblasts. Derivative 3 was a chalcone only with IC50 of ~20 µM and has a very interesting signature where it enhanced apoptosis in HepG2 by stimulating the expression of downstream execution caspase 3 without affecting neither p53 nor initiator caspase 9. In spite of the structural similarity between compounds 6 and 7, compound 6 discerned itself with a unique IC50 of ~ 10 µM. Results: The antiproliferative activity of derivative 6 could be attributed to its unique capability of formation of free radicals such as phenoxide radicals which arrested the cell cycle through enhancing the expression of p53 and induced apoptosis by induction of both caspases 9 and 3. It was the only investigated derivative that inhibited the tyrosine kinase activity by 89%. Conclusion: The antiproliferative activity of the compounds under investigation considerably depended on the nature of the substituent at position 4 in phenyl rings of both chalcone and Schiff base fragments. Derivative 6 with electron withdrawing chlorine substitution on the phenyl ring of Schiff base fragment and an electron donating methoxy group on the phenyl ring of chalcone fragment was the most active member.

scholarly journals Imidazole and Azo-Based Schiff Bases Ligands as Highly Active Antifungal and Antioxidant Components

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Siham Slassi ◽  
Adeline Fix-Tailler ◽  
Gérald Larcher ◽  
Amina Amine ◽  
Abdelkrim El-Ghayoury
Keyword(s):  
Radical Scavenging ◽  
Pathogenic Fungi ◽  
Imino Group ◽  
Absorption Bands ◽  
Visible Absorption ◽  
Full Characterization ◽  
Highly Active ◽  
Azobenzene Moiety ◽  
Base Fragment

We describe, herein, the synthesis, full characterization, and optical properties of four different ligandsL1-L4which associate an azo group, an imidazole unit, and a Schiff base fragment. The UV-visible absorption bands are characteristic ofπ→π⁎andn→π⁎transitions with an additional charge transfer between the azobenzene moiety and the imino group. Finally the determination of MIC80values against pathogenic fungi such asS. apiospermum,A. fumigatus,andC. albicansrevealed that these ligands have effective antifungal properties with highest activities (MIC80) onC. albicansfor the azole based ligandsL1-L3. DPPH radical scavenging of the studied ligands was also tested.

scholarly journals Occurrence and genetic diversity of pigeon circovirus strains in Poland

2014 ◽  
Vol 62 (2) ◽  
pp. 274-283 ◽  
Author(s):  
Tomasz Stenzel ◽  
Daria Pestka
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Capsid Protein ◽  
Immunosuppressive Agent ◽  
Amino Acid Sequences ◽  
Amino Acid Similarity ◽  
Capsid Protein Gene ◽  
Base Fragment ◽  
Polymerase Chain ◽  
Young Pigeon

Pigeon circovirus (PiCV) is an immunosuppressive agent widespread throughout the world, which causes a disease in pigeons called Young Pigeon Disease Syndrome. The aim of the study was to evaluate the prevalence of PiCV in Poland and investigate the genetic diversity relative to other known PiCV isolates. Samples from 152 pigeon flocks (88 flocks of racing pigeons and 64 flocks of fancy pigeons) from various regions of Poland were tested by polymerase chain reaction and an approximately 326-base fragment of the capsid protein gene (Cap gene) of the virus was amplified. The average viral prevalence was found to be 70.3% (76.13% in racing pigeons and 62.5% in fancy pigeons). Among the obtained positive samples, 21 were selected for sequencing and a phylogenetic analysis was performed. It was found that the majority of Polish PiCV isolates, to varying degrees, are related to isolates occurring in Europe. It was also observed that the Cap gene is variable and mutations often occur in it, which impacts the amino acid sequences in the capsid protein (nucleotide similarity averaged 86.57%, amino acid similarity averaged 89.02%).

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